Well i can say that perosnally ive trained both ways. For my first couple years of lifting i only went to 90 degrees, and when i did switch over to full ROM bench presses, i found out what I had been missing. My BP #'s increased rapidly and i found i was hitting people in football with my hands much more forcefully.
If youre an athlete then it will definitely benefit you, because of the stretch shortening cycle.
BOTTOM LINE: Yes strive for full ROM, its the best thing you can do, of course maybe get the shoulders checked out, but depending on what kinda pain youre talking about it may not even be a problem, because i know that when i made the transition all of my muscles were very tight @ the bottom portion for the first couple of weeks.