Personally, I think it was a mistake.
It solidified the party ticket.
Having a vice president that came in second means that, if something happens to the President, the country will be led by someone qualified.
As far as checks and balances go, the vice president is the tie breaker in the Senate. With the 12th amendment in place, that vote is essentially the President's vote.
We would still have a system of parties but the dynamic would be dramatically different.
Finally, the original system meant that most Americans would feel represented. Yes, the VP has little power but they can have lots of influence.