I can't really speak to traffic because I rarely drive, but I do agree there needs to be more investment in rapid transit. I rely on the red line/walking to get to and from my office. It is the only line I would consider living on.
But I did want to add that it isn't only the north end that was cut off. I doubt the resurgence of the Sea port area/"innovation district" would have happened if it hadn't been for the big dig.
They should have eliminated the Big Dig completely and spent the money on increasing rapid transit capacity.
That said, eliminating the elevated highway that cut the North End off from the rest of the city seems to have been a major boon.
[1] http://en.wikipedia.org/wiki/Law_of_demand
[2] http://www.boston.com/news/local/articles/2008/11/16/big_dig...