Substantively, I don't have strong feelings about Kaine either way at this point. But on a more practical level, did Obama and his vetters watch Kaine's State of the Union rebuttal back in 2006? After watching it, I wrote that Kaine's left eyebrow is "too distracting for the party to ever put him on national television again," prompting the Columbus Dispatch to call this "the site for chatter about 'Tim Kaine's crazy eyebrow."
You really have to watch the C-SPAN Real Player video with the volume off to understand, but here's a screen shot that gives you some sense of what he looked like:
It's true that (a) Kaine got elected in Virginia anyway and (b) vice presidential nominees probably don't have a significant effect on election outcomes. But given that national politics is centered around television, do you want someone who looks that strange on TV on the ticket? Maybe I'm being superficial, but it seems like a legitimate strategic question.