One thing you'll want to keep in mind is that depending on your class, some of your story quests may force you to use one or more certain companions, or forbid you from using others. That means if T7's your favorite and Kira's just collecting dust, you might have a tough time when your story forces you to bring Kira (and she's still in her Coruscant-level greens while you're level 30+). So far I've noticed the Jedi Knight and Trooper stories are bad about this. So, either spread the love (which can be expensive) or be prepared to shell out some credits to boost a required companion's gear quickly if the worst happens.
This was along the lines of what I was wondering. It seems like, ultimately, there isn't too great a penalty for mostly playing with only one. However, what if affection is low and I don't buy trinkets for them? Do higher level missions fail a lot with low affection?