First, it wasn't just the addition of the Wild Card. It was divisional play and an extra round of the playoffs to go with it. That is a HUGE change, which was also hugely successful.
Another, interleague play. There are still some opponents of it, but it'd be hard to argue that it hasn't been good for the game.
There's really two major black marks against Selig.
The strike in 1994, which was right after he took office (when he was only "acting" Commissioner). But since the strike, revenues of baseball have skyrocketed. I don't know the exact numbers, but it's something like quadrupled during his tenure. Attendance, too, is up. And it made this recovery thanks in large part to his changes.
The other obviously is the steroid issue.
This one was mishandled at pretty much every level. But it's hard to argue with Selig's policy in recent years. Despite all the media attention on baseball, MLB now has the most stringest testing in US sports. People hold baseball to a higher standard than NBA, NFL or NHL. But it isn't only a baseball problem. But it's a problem on the mend, not getting worse. Thanks, in large part, to Selig.
Again, I'm not saying Selig was a saint, or never made mistakes. Obviously he did. But I don't think it's cut and dry. In a lot of ways, baseball is much better off for Selig being commissioner. In other ways, perhaps worse. Like I said before, I'm on the fence about it.