Ben Smith has a good story on how the Obama political braintrust's decision to dismantle the Democratic outside interest group sphere-o-sphere in 2008 is having ramifications in 2010, as Republicans massively increase their independent efforts.
Obama wanted to control the message, but his campaign also evinced a distaste for the seeming gaucheness (my characterization) of the outside groups and their pesky insistence on doing things the way they wanted to do them. David Plouffe may be a modest guy, but he was a shark when it came to this stuff.
A financial disadvantage in 2012 might not be avoidable for Democrats unless Obama and his team decide that outside groups can be helpful. They will never overtly make this announcement, of course, because it would cast them as hypocrites. Instead, you'll hear things like, "Oh, well, we don't control these groups and don't endorse them." And you'll see publications like Politico's Playbook be used to provide friendly hints to these groups about targets and messaging.
Obama faces another potential funding problem in 2012, this one more direct: a lot of folks in his major donor network are going to need a hell of a lot of care and feeding before they sign back up, particularly if there is a credible business-friendly Republican candidate who is running against him. Obama's just not going to be the candidate of Wall Street in 2012. And it's hard to see, at this point, his low-dollar network producing the same returns they did in the heady years of 2007 and 2008. (That said, President Bush was able to top his 2000 campaign totals significantly, but he did nothing to alienate small and large donors in the first four years of his presidency.)