Can't. Read. A. Thing.

Engineers tend to be good at engineering. Not architecture.

For example, where are the closets and clothes storage for Bedrooms 2, 3, and 4?

Why the confusion of doors at the entry?

Why step into the house and see a runaway corridor in front of your eyes?

And the make-believe kitchen?

There are so many things wrong here, there isn't enough posting space. You can do better if you really want to do so...

Good luck on your project.

Straightforward plan for the most parts. Not terrible. The kitchen can be improved upon greatly. Will laundry be done there too?

What's the family make-up, what's the land like? Has your lifestyle been considered during the design?

You say you can't put your finger on what's wrong. I think I can start. "the only thing we changed is having the storage near the hallway to be converted to a powder room and a toilet added to the 2nd bathroom"
Hasn't quite been changed. The storage remains storage, and the 2nd bathroom still has no toilet...

But in trying to find out what's 'wrong', complete the sentence: "It feels..."
big, small, open, closed, disjointed, detached, overly connected, open to outdoors, crowded, personal, impersonal, ...
When it was designed, did you discuss what you'd like to achieve? Privacy, space to work, entertain, ...?

Can you remove one door so that you enter through the porch?

Good idea Alan

Please forgive me, but that has to be one of the most insipid and banal floor plans I've ever seen.

I don't see closets on three of the bedrooms. I don't see a laundry room or a pantry for the kitchen - they might all be there but they're not labeled. The only room with a proper vestibule is the back left one. The foyer is made somewhat awkward by the porch door. There's no coat closet at the entrance. There's a big blob of blank, wasted space behind the dining room, and the first bedroom on the left spills out into this area.

There's also no back door, but that may be by design.

With all the ready made house plans out there, why this?

Is there really a wall between the foyer and the porch? Why?

Looking at the floor plan, one wonders if there is anything attractive about your site or land on the sides or rear of your house. This design simply closes off the house to the sides and rear, and the only "usable" outdoor space is on the front porch, which conflicts with your entry door.

You really can do better than this if you want to.

She, you're right to think that this plan seems not quite right. There are a number of areas, as others above have pointed out, that need help. The thing with a house plan is that you can't consider a room in isolation, or even the interior in isolation. You have to consider each room, the entire interior, and the entire exterior as a whole, together at the same time. This is a talent and a skill which not everyone has. I don't have it either : ) . You need a person of design talent, whether it's a professional (an architect) or a skilled amateur.

How many people are in your family who will be living here, and how long do you plan to live in this house?

What sort of a climate do you live in? If you live in a warmer climate, your plan does little to make the outdoors accessible from inside the house. If you live in a cold climate, your plan does little to provide an enjoyable, welcoming house in which to spend much time.

This looks like a modular home, perhaps factory built in pieces. Is it? (Could that explain why an engineer is designing it, rather than an architect?)

Looks like a very typical UK/European plan. Likely would have wardrobes instead of closets. Laundry would be a machine (or two) in the kitchen, under the counters.

It reminds me of a college dormitory floor.

Ew mcmanson. I'm talking about ranch house plans, historical house plans, et al. Regarding the subject at hand, we have an aversion to the same things.

Why are you begging the question by inserting mcmansions into this? Nobody has said anything about them.

Do a walk-through for the occupant of each bedroom ... run them through common tasks like bathing, dressing getting a glass of water in the night, etc.

Where will the occupant of Bedrooms 2, 3, and 4 be able to use a toilet? There is one visible in the plan and it's accessible through one of the bedrooms, in the en-suite bath.

Where are you planning to build?

Looking at the plan reminds me of the old joke that God must be an engineer. Because when He designed our bodies who else would run a sewer through a recreational area?