My first rule of thumb is how long you expect to live in the home? If you are short term, pay lots of attention to making the house as generally appealing to the broadest possible market. If you are long term, 7 years or more, then I'm more inclined to suggest you do what pleases you.
4 bedrooms or more will always find a market in Bellevue. 3 car garages are common in the upper price ranges and are a sought after feature.
The "magic room count" tends to be 4 bedroom, plus den, plus bonus with 2.5 or more baths. This is the most sought after scenario for most of my buyers. Garages are popular, but they are less expensive to add than finished rooms, so it could come down to your budget too.
As you can see there is one home there that offers 2 car garage. A compromise might be 2 construct a home with a 2 car garage that has additional storage, the question will come down to how long do you plan to own the home -- if for a fair amount of time, then the value is there for you to build it as you prefer. If you plan to resale within next 5 years then you might go with the smaller house and bigger garage since often time people seeking a 3000+ sf home expect (or at least hope to find) a 3 car garage and if that is your competition.....regardless you have the location, location, location that will prove very valuable in the end!
Best of luck!
Definitely go with a 3 car garage...buyer expect anything over a 3 bedroom to have a 3 car garage and the 5th bedroom at that square footage will not be expected.
Good luck on the build!
Heidi & Michael Syltebo I Coldwell Banker Bain I Above & Beyond Real Estate Representation
425.652.6573 I EastsideHouseValues.com