I don't think the Twelve were chosen based on their influence in the first place. I seem to remember more about James and Barnabas and Timothy than I do about half the Apostles (by name anyway) in regards to what's said of them in the Bible. They were chosen because they were chosen (I love me some tautologies. Still, I would guess they were chosen because played the roles God wanted them to rather than because they were titans of the faith with massive followings; faithfulness seems more valuable to God than what we perceive to be results). God rarely does things in the way we expect, nor does he make His decisions based on our ideas of bests. Israel wanted Saul. David was the least of the sons of Jesse. Etc.
Would it make more sense for Paul to be among the Twelve? Only with respect to the expansion of the early church. He didn't meet the criteria set forth by those filling the hole left by Judas (as Abba San pointed out). And "think God should have" is turf I never want to step on. God's wisdom often seems like foolishness to us. The best we can do is stay true to biblical teaching, not our predictions of best (after all, it would have been a long time until Paul could be counted among the Twelve if they waited until he proved himself and saw the results of his work), and that's what Peter and company seemed to have done in choosing Matthias to take Judas' place.
So, I feel pretty safe saying Paul shouldn't be considered the replacement for Judas, but that's clearly no mark against him or his work.