As long as it works for you, there's nothing wrong with not using your index finger. My playing style is very similar to Geddy's, but his "primary" finger seems to be his index, and mine is my middle. Doesn't change a thing, I can still crank out all the same sounds, for the most part. If you can build up the strength and dexterity with those two, the more power to you. Personally, I don't thing I'l ever use 3 finger technique, because it's not worth it to learn something just because I "should". Same way with you and your index finger. If you feel like you can't play well because of it, then practice shouldn't be as difficult. It's hard to practice something that you don't really care for, but if you really want to learn it, it will come.
IMO, YMMV, ETC, BBQ
Fender Jazz Bass #1029