The Skydome certainly isn't an ideal baseball stadium, but seating capacity isn't really one if it's issues. I've been going to Jays games since the early 80's and was at the Dome for the ALCS and World Series games and the atmosphere was fantastic for those. Even for regular season games in the early 90's, you had to pay double face value for tickets in the 500s for almost every game. The strike unfortunately killed all the momentum the team had built up over the previous decade and they have struggled to get back even to where they are now.Most baseball stadiums are around 40,000 capacity maximum. Skydome can fit over 70,000. But of course, even at 40,000 it wouldn't raise the 20k-ish level each game. Of course a new stadium might. Too bad we won't see one in a long, long time.
I imagine the Jays will likely never see their popularity back to those levels, and I don't really think a new stadium will solve much of their issues.
EDIT: Also, the Dome can't fit 70k in it's baseball configuration. I think the max it can seat is around 55k for that.