lugged vs. tig?
rack/cable/water bottle bosses?
It might be best to get 2 bikes, rather than trying to build a compromise bike (e.g. a bikesdirect fixie and a custom cross/touring/road bike)
Or just make sure you have your builder set up the bottom bracket and dropout spacing such that you get a straight chainline as a fixie, but still have the ability to use gears as well.