When you're starting to plan, concentrate on the layout. (You're not moving the kitchen after it's in.)
Maximize what's most important to you. bedrooms, window, bathrooms, kitchen...
That said, I'm glad I spent a little extra on certain upgrades to my main room. It's the room I entertain in.
I like that I added a bathroom off the master bedroom.
I'm enjoying my finished basement, but I consider it a luxury; my storage could have stayed in an unfurnished basement, the bedroom is only used for sleeping over yomtov, and the toy and play area might have found a place on the 2nd floor.
Central air changes the way I think about air conditioning. Now it's more 'climate control' like heating.
Also, not everything has to be done in one shot. If you can't afford everything you want, save some things for round 2. The basement often can wait. Even the kitchen- you can put in a cheap kitchen with your old appliances and upgrade years later. But make the layout you like now.