It's always tough to decide what tradeoffs to make when building, but you should try to identify which upgrades can be done later, and which ones should be done now.
The doors could be done later, and you may be able to get some money back from the old ones. The doors that they put in new houses don't cost much, so the upgrades are likely quite expensive, as you say. Even if you don't get anything from the old doors you won't be out of pocket much, and you can save up until you have enough to change them.
I'm assuming you are talking about a half-wall instead of the banister. Again, if you have experience with basic construction or woodworking, this is something you could do yourself, but it might be a bit messy. If it is a half-wall and it isn't a safety concern, maybe it could be left out and you could install the railing when you can afford it.
Granite counters can be quite a bit more than your standard countertops, but can be very beautiful. As well, the kitchen can make or break the sale of a house, so you'd be spending money in the right room for re-sale. However, it might be possible to get rid of the exixting counter and replace it down the road, but you'd be wasting more money than on the doors, most likely.
I'll assume you meant "look good" and not "look goofy" here. Cabinets are a major expense and you should look to put in the ones you like here, because it would cost far too much to get rid of these. Again, it's the kitchen, so it's likely money well spent. My wife and I looked at over 200 houses before we bought the one we did and the biggest turn-off was the kitchen cabinets. This is where I'd likely spend the money now if I had to chose.
One thing to keep in mind, though, is that you will have a lot on your hands with a house so you may not have as much free time to do your own upgrades as you would hope. It all depends on your schedule, energy level, and the number of kids that like to 'help' you with your work...
I do agree with the above suggestion about insulation, but I think that crown mouldings can easily be put on in a weekend with little more than a mitre box and saw. The mdf mouldings are the same density as pine, are pre-primed, and a lot less than solid wood mouldings. Best of all, nobody can tell the difference once they are installed and painted.