First rule, Don't let your builder tell you "You don't want that", when you have asked for something. I let my builder talk me out of a few things (minor) that I wish I had not. I do regret that.
I love looking at floor plans. We built our house 13 years ago and there are a few things I would change for sure. Looked good on paper but in real life practicality, not so much. Do-able, dont get me wrong. Just not the way I would do it now.
I like the master layout. You can always insulate the common wall between the great room and master bed room. Love the separate commode room. One suggestion I would make is to take away the angel of the closet, giving the commode room a flat wall and installing a solid wood (or solid core) pocket door here, rather than a swing in door. While it looks ok on paper, having those two angles in the closet limits the actual hanging space.
Another thing you might consider. If you want a closet system in your closet, design one on one of the websites (I think I used easyclosets.com or have a closet designer come give you a plan. Then, instead of using them, print out the design and have your cabinet maker (rather than the trim guy) custom make your built-ins. We did this last fall and it was half the price of the closet systems cheapest material.
I see you have a pocket door at one end of the pantry, I would put one at the other end too. Again, go solid, either wood or core.
I don't like the whole walk in closet/mud room/pantry/utility layout. I would leave the pantry where it is and I like a "mudroom" entrance off the garage. I would have it like a galley mudroom though, with your built in's to one side. Do a search on mudroom design for inspriation how you want it to look exactly before they are ready to build it.
I would increase my laundry room to accomodate the closet, if possible, and the standing freezer. One larger room that can accomodate everything is better than many smaller rooms,with this and that. Again, I like quality pocket doors and would put them on the utility and perhaps on the 1/2 bath. If they are not security doors, or a piece of art, for me, I like them out of the way.

while I do not really have plan modifications, I would encourage you right now, especially for MN, to start thinking about how you want to build the shell of this house. Focus on a goal, energy consumption, etc. DO NOT let the builder tell you 2x6 walls with r-21 batts is efficient. It is barely a code standard in your area, and in less then a year, will not meet energy code any longer.
No body likes spending money on the shell, but your shell is the ONLY source of payback any dollar in your house will give you. $30,000 cherry cabinets do not reduce your monthly bills. $5000 more worth of exterior XPS sheathing will. Talk with your builder. Look into air sealing as it is SO important for new construction in your cold climate. Look into exterior foam insulated sheathings, 1-2" min. Look into r-50-60 insulation in the attic. Spending in these areas will save you money over time and will most likely pay for itself rather quickly in your climate.
There are too many questions on this forum by people asking what insulation to use, even though it is way too late in the game to make cost effective energy efficient changes. It needs to be figured out and detailed up front before construction begins.

Nice plan but a few things you might want to think about before finalizing:

1) This is a very complex shaped house design (i.e., lots of exterior corners). Be aware that the least expensive home to build is a basic rectangle and that every variation from the rectangle increases costs. All those juts in-and-out increase costs per square foot because they result in a higher ratio of exterior walls to interior square footage which means more framing material, more insulation, a more complicated roof-line and foundation, etc. Not saying you should change a thing... just thought you ought to be prepared for the sticker shock you may receive when you start getting bids.

2) You kitchen island is positioned so that any dirty dishes in the sink will be on display to anyone in the Great Room. No problm if you're the kind of housekeeper who keeps the sink area spic and span at all times. Me? I would want the island turned so that the raised section helped to hide my sink from the great room. But that would pretty much require an entire reshaping of the kitchen and thus the rest of the plan. So, you will probably want to keep it as is.

3) No windows in the kitchen itself? Patio deck doors and great room windows may be rather far away to provide much natural light for kitchen. You don't mention the direction your house faces and, if the wall that the fridge is against is a north wall, you might not want any windows there. But, in that case, I would question placing your screen porch on that side of the house.

4) The laundry room and mud room seem a bit cramped...especially for a home with three kids. Since the garage juts forward anyway, unless you're already running up against lot-line setbacks, consider pulling the snout of the garage forward another couple of feet and then extending the mud room and laundry room forward an equal distance into the garage to enlarge them. The cost to do so should be relatively minor compared to overall cost to build because, although you would be adding a bit of square footage, you would not be increasing the complexity of the design in any way.

5) Make ABSOLUTELY certain that your pantry is wide enough to accomodate the freezer you want to put in it... not just the one you have already. Measure the depth of the freezer you want to purchase and then add about three inches. A freezer can't sit right up against the back wall. You have to leave room for air circulation and you don't want the freezer sticking out so far into the pantry aisle that you can hardly squeeze past it. I thought I had left plenty of room for a freezer in our mudroom/pantry but freezers today are bigger than my old one. Our new one just BARELY fits. I have just exactly enough space between the freezer and the counter across the aisle to fully open the freezer door... nor an inch to spare. It works - but if my pantry/mudroom were 6 inches wider, it would feel a whole lot more spacious! Also, speaking of freezer doors, you probably don't want to put the freezer right up against the side wall or you may not be able to fully open the freezer door. It needs swinging room. Finally, make sure that at least one of your pantry doors is wide enough to get the freezer in and out of the pantry! We had to have the interior door of our pantry reframed to 36" wide b/c our builder installed a 32" exterior door on the mudroom/pantry instead of the 36" wide one specified on the plans... and we didn't notice THAT error until after we fired him and took over the build ourselves. (By that time it would have cost us thousands to reframe the exterior wall, get a new exterior door, have the cabinets on the exterior walls remade to fit the reduced space, etc., etc., etc., GRRRR!!!)

6) Similar issue to above...how much room is there between your refrigerator and your kitchen island? Unless you get a "counter depth" fridge, your new fridge could stick out as much as a foot beyond the edge of the surrounding countertop.

7) Have you thought about furniture placement yet? Bedroom 2 looks a bit problematic b/c the best position for a double bed seems to be up against the bathroom wall. But that would mean one would have to walk around the bed to get from closet to bath. Perhaps you could flip the bathroom vertically so that the tub is against the front wall and the bathroom door is close to the closet door.

8) In bedroom 3, would the door fit on that little angled section of wall? If so, I think you'd find it easier to place a full-sized bed and other furniture in the room. Besides, that would give you a nice section of wall space in the landing/hallway for a bench or maybe some book cases.

9) Not sure I agree with zookeeper93 about combining the closet and laundryroom (especially not if you can increase the size of the laundry room.) It can be nice to have a separate closet that isn't subjected to laundry room lint. And I definitely would not want my freezer in the laundry room area. Guests helping me cook sometimes need to access the freezer when my laundry room is simply not presentable. LOL!

10) I do agree with zookeeper93 tho that the angles in your master closet are going to limit the actual useable hanging space. Unfortunately, I don't think you have room enough for a door into the commode room if you try to just straighten out the wall by the commode room. I can't tell what those two little niches are between the master closet and the master bedroom (seats?, inset bookcases? art niche's?). If it were me, I would get rid of them and incorporate that area into my master closet. I would also swap where the shower and commode are. I think that would give you enough room for a closet with nice-sized USEABLE his/hers sections. Maybe something like this with a pocket door to the master bath:

BTW, you need to be very careful when using pocket doors to make sure that you're not planning to attach closet rods or the supports for something like an Elfa closet system to the walls where the pocket door "hollow space" is. Remember, there are no STUDS in that space and you need STUDS to support the weight of clothing hanging on closet rods.

If you're concerned about sound transmission from the living areas to the MBR then, in addition to insulating common walls, you could install a second doorway near the study, creating an inner hall/vestibule. Might be difficult with those angled walls, but it would create a second barrier.

Actually, if it were mine, I might prefer the door to the study to be within this inner vestibule as well. Depending on how you work and use your study, an extra sound barrier might help there too.

Thanks for the input! Lots for us to think about.

I also thought all the angles in the master closet and office weren't quite right. Thanks for the updated pic of that area. I like that SO much better.

I am finding this really hard to see the house I am going to live in, on paper. I just can't picture it. I almost think we need to find an existing house and copy it. Or at least use it and make some changes. How do you know when the plan is 'just right'?