Homebuild,
It looks like you are in an advanced stage of the design process. If you want accurate comments, I would like to be able to see the dimensions. Can you post bigger drawings? A PDF is better.
Do you have an elevation?
So far, there a few things that I do not like and many that I like - and it also depends on the specific circunstances.

Oh yeah. I have everything. I will try to get the elevation as soon as possible. But for now, here are the pdf's of floor1 and floor2. Thanks a lot for looking into this.

Floor 1 PDF:
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Floor 2 PDF:
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There are only a handful things that pop out to me-
1. Imagine backing a car out of the single garage- since the garage behind it bumps out, you could easily back into it, or scrape the side of the wall trying to make the turn. Also, it's a bit small if you wanted to pull a vehicle in and open the car doors. If this is intended for a tractor or golf cart, then it's probably ok, but I'd make it wider to solve both problems.
2. The exercise room is a nice addition but it will be nightmare getting any equipment in there due to the tight hallway openings and offset door. Consider a double door or move the door next to the fireplace- that would add the wasted hall space into the excercise room.
3. You might have the same problem moving furniture in the master bedroom due to the tight corner entrance. Did you consider having french or sliding doors to the patio?
4. The doors closing off the master closet might be overkill? How often would those be used since there is already a set closing off the entrance leading to the closet and bath?
5. You'll have to move out of the way or sit on the toilet to close the door to the toilet room once you are in there! Consider making the door swing out instead of in.

This is truly a nice, well-thought-out plan and you are really on your way to planning a nice home!

A few things popped out at me. And this is high-level; I've not caught up on dimensions yet.

1. Guest BR and dining: If only there's a way to flip the locations of these two. Guest bedroom is accessed by a hallway between the kitchen and dining. As a result, dining is quite far away and guest is sitting sort of inbetween.

2. You need to ask yourself if you'd ever use formal dining. For one, it's not much bigger than casual dining and secondly, it's very far in the current plan.

3. Music room and exercise room. In addition to exercise room being planned via tight hallway, it seems to be a very small area. Exactly what are you planning there? IMO it should be at least the size of music room. If you're into working out, then you'll add equipment over years. If you're not then you're better off without it.

4. In the kitchen, sink is at an angle from dishwashers. You need to be careful that they can open with you standing in front of the sink to load them. Even then it's been experienced that this arrangement is less ideal than both being in same line.

5. Music room seems to be planned for just keeping a piano etc. It has no soundproofing therefore it seems like it is a casual rec room, where music will be played. Why not make it a bit more open to family area? That way, those in the music room will maintain visual contact with folks in family area. Otherwise, sound will travel but person will be hidden from sight.

6.What is the triangle between family and Master BR? Is it an Atrium? It's too small a space if it is.

On the upper floor, things look ok though the two bedrooms on the right of stairwell are too far away from the staircase.

It is indeed a well-thought-out plan.

What I do not like:
The garages. If you did not have the small one, the kitchen could have windows. The 3 car one, blocks the kitchen view.
Maybe the kitchen will be dark depending on the orientation, since you have a wide porch.
When you have a one story house sometimes it is difficult to place windows in the kitchen but when you have a 2 story home a good designer should be able to figure it out (This does not mean that the designer is not good, so far I like his/her job)
I think you can shift that garage to align the wall with the mud, and maybe make the small garage a side load. This will not change the front elevation.
The mudroom size and setting. It is too small and then you have to go to the laundry to use the cubbies. By the way, the location of the laundry door is not ok.
The dining is a bit far, isolated and small. By the time you discount wall thickness the dining is 11'-7" wide. You will have a gigantic piano and a tiny table (just kidding)

What I like: the thicker walls where visible.
The STAIR!!! and the Juliet balcony.
The entry/little foyers at several main rooms, also the niches.
The butler's pantry location (too bad that it will be dark.

What I am not sure:
The corner fireplace and its raised hearth.
The Powder room ceiling and shape. Hopefully it doest look weird.

About the drawings:
I like the job that the draft person did. It has some flaws but it is good, overall. Sometimes is is a bit misleading in the way he shows the dimensions.
Do you happen to know what program he uses?

Is this a custom design or a stock plan? May I ask who the designer is?

Good luck, and show us the elevations when you have the chance.

1. The exercise room is actually a craft room. There wont be any equipment there for now. but you are right, if we could make it a little bigger and have wider doors, we can move exercise equipment there in the future if we need to.

2. Good point on making the 4th car garage wider. I am going to do just that

3. We did not think about having French door from the master to the patio. You think that space is too small to move furniture?

4. We might remove the doors that open into the master closet. I did not catch that until you mentioned it.

5. Good point on making the master toilet door open outwards.

6. Formal Dining is too far from kitchen and too small? I did not think about either of these. Since we wont use it on a regular basis, I figured this would just work.

7. I am not happy with the kitchen layout. I am thinking about making the Island bigger and eliminating the wrap around with the bigger sink. I am breaking my head over a better kitchen layout and the fact the kitchen does not have windows is not something that I am excited about. I think it might be too late to put a window there although I will check with the designer.

8. The triangle between the family and Master BR are fireplaces. I hope that I am referring to the same thing that you asked about.

9. The design I think was done in Autodesk.

Questions:
How can we make the music room more open to the family area? Thoughts?
Any thoughts about a better kitchen layout?

Thanks for all your comments. If you have more, please let me know. But I am still not happy with the dining room size and also the current kitchen layout.

Re. opening music room to the family area, you can do that by relocating the coat closet to the front of the foyer. Perhaps close to where the double door to study is. That would open up the wall to the family area and define the boundary of music room and the entry.

Regarding kitchen layout, I do not see any way to add more windows unless you relocate it or take off the back stairwell and other structures. Alternately, you could create a sort of "courtyard" like space between the kitchen and the garage and attached stairs etc. to add windows to the kitchen.

Even then, the kitchen view would be looking at the garage wall.

I would take your kitchen plans over to the kitchen forum for input. There are some VERY talented people there and kitchens are their "thing".

The 2nd floor bathrooms and the butler's pantry would be helped by some natural light. It looks like there is room between those rooms and the stair to run the tube for a Solatube fixture down to the butler's pantry.

A house this big deserves some formal and/or private spaces. I rather like the music room to be a little closed off. It makes it function almost as a old-fashioned parlor. I think if you open it up to the already large family room, entering the house will feel like entering a cavern.

I dont get the fireplace in the music room. It really wont be visable with with a grand piano sitting in front of it.
If the fireplace is in use, couldnt the heat cause damage to the piano? Dining room too remote. Master bedroom access would be better if off music room....seems strange to have a huge house and all these hallways (lots of hallways)and then have to go into the living room to get to the bedroom.I would increase the size of the exercise room be extending it into the hallway (and up against the back of the fireplace) and making the entrance into the room across from the closet (eliminating ANOTHER hallway)

Overall I think the design is really great and would love to see the elevations. But can you stand a few more comments about possible tweaks?

1) If you swap the location of bathroom and closet serving bedroom on the front right upper side of house, you could add a window to the bathroom for natural light.

2) Same thing may be true for the closet and bathroom serving back left upper bedroom tho in this case the slope of the ceiling might prevent that. I've sketched a possible revision below.

3) What's up with the zig-zag hallway upstairs? Did you mean to put in a door at the end of that hallway to reach the front left bedroom? Have you thought about turning that bathroom horizontal (and against the outer wall so you can put in a small window) and putting the closet beside it so that what is now the zig-zag hallway becomes a rectangular space? Since the bedroom room is at least 15' wide, you have room for a nice wide bathroom and a nice wide closet. Then you could turn what now seems like a wasted hallway space into something like a reading nook. If you want the front left bedroom to have easy access to the back hallway, you could even put in a door from the bathroom opening into the reading nook area.

4) Re the "exercise" or "craft room" downstairs. Since it is on an outside wall, have you considered patio doors in place of the windows? If it was ever used as a craft room, that would make it easy to get equipment in and out. And, while it would mess up your master closet plan, it might be good to try and figure out some way to put a doorway from exercise room into the closet so there is access to the masterbath.

5) And finally, instead of the rather long hallway between music room and exercise room that ends in an odd "deadend", why not just incorporate all that space into the "exercise room". Nothing wrong with an odd shaped exercise or craft room.

Anyway, here's a sketch showing possible revisions to the upstairs. Just some suggestions as I really do like your house!

Thanks for all comments. I think the general consensus is removing the hallway behind the fireplace and I am going to do just that. That space can be incorporated in to the music room as you both mentioned. I also like the idea of switching the bathroom and the closet. I appreciate the fact that you took time to sketch that out and also the reading nook. Regarding swapping the closet and bathroom in the second bedroom, it is not possible because of the roof line.

Keep them coming. This is really helping me tweak the current plan.