The people on this forum can give you really great advice on kitchens. Re-post your questions there. http://ths.gardenweb.com/forums/kitchbath/

Can you change the exterior walls? If not, consider moving the fridge into the pantry and center the island with the bump out.

Other's have commented on the layout so I won't bother

I will say though do not stagger cabinet heights. One height, all the way across. Take it up to the ceiling if you can so that you can maximize space and make the room feel taller.

Shorten the depth of the bump out and push the stove back into the former pantry. Widen the pantry cabinets opposite the sink.

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Do you have a signed contract with this builder? It seems like the layout is simply not going to work for your family? With all the variations you mention, I think if you aren't locked in, I would keep looking because this kitchen is tiny and pretty limited in terms of making changes that will work. The reason most builders don't want to make "structural" changes, is because they don't have the engineering done for those changes and that makes this a "custom" approach which is always more expensive. So, seems like you have a pretty big choice to make. For sure I wouldn't want my refrigerator far from my sink. Pretty basic principle.

I just see so many red flags here and that worries me for you and your family. I hope you take a step back and really assess if this is right for y-all. Hate for you to have a long term mess. Praying for the best!

OK, glad you feel comfortable, that means a lot. Do consider moving the refrigerator to the wall currently showing the range top and the range top to where the refrigerator currently is. You use the refrigerator most in a kitchen so that proximity is key. Good luck.

Where are the double ovens in your current plan? Pushing the stove back would allow you to center the island with the window/sink and also allow you to move freely around the island. The corner circled is pretty tight so you'll probably have to reduce the island size, which makes the breakfast nook even bigger. Just seems like the kitchen is unnecessarily scrunched in the corner when the adjacent room is massive. It's your house though. You know what works for your family so go with your gut.

How often do you put food from the cooktop directly into the oven? For me, it's once a week on Pancake Day. If you don't do it very often or with a regular routine, swap the wall ovens and refrigerator. You can bump back into the space you've designated as pantry.

That leads me to my next question: how wide is the pantry. Looks like about 4'? Because honestly a well-designed reach in pantry or shallow wall cabinets can be just as practical as a long narrow pantry, if not more so. Particularly since you're looping around into the breakfast nook with base cabinets I would look into wall pantry designs if I were you.

If you take that advice, you can use the remaining section of the pantry for the powder room (toilet behind cooktop, sink across from it, pocket door) to create a bit more space in that hall.

Here's another thought, since you mentioned kids. Instead of a continuous run of cabinets from the kitchen into the breakfast nook put the cabinets on the other side of the window in the breakfast nook. That can be the snack cabinet with anything they are allowed to help themselves to. I have a snack drawer in my kitchen with seeds, nuts, crackers, granola bars, dried fruit. Mine is at the end of my island for easy access without getting underfoot of the cook. There is a cupboard adjacent in the island with their plastic cups and wooden snack bowls. Yours could be over in the far corner. It would relieve congestion in the kitchen island area.

Seems to be a whole lot of compromising for a dream house. If the kitchen is that important to you, usually the Architect starts there. They don’t leave it to hind end leavings in space and budget.

Just an update - even though its a year later.. the kitchen came out exactly how we wanted. Thanks for all of your help on here!