Well, I'd say simply having to register to be able to sell BTC would be an issue.  FinCEN, as much as it has a lot of bad things at its disposal that it has not, in fact, done to date, has a fairly lengthy history of creating regulatory uncertainty and then suddenly prosecuting some practice that has been, to date, tolerated.  While I am not a full-bore anti-government loon by any stretch of the imagination, and in fact, FinCEN's public official statements to date have been actually pretty welcome and reasonable, there is still an environment of regulatory uncertainty.

In some senses, this is good.  Sometimes, you really don't want the government all that interested in what you're doing at the moment.  However, it makes it rather difficult for large-scale money and venture capital to make long term decisions when they are considering rolling out physical infrastructure and other things that can't be rolled back and turned back into money should the situation change.  A lot of the kind of tech necessary for large-scale investments in Bitcoin is going to be stuff that is useful for nothing other than Bitcoin.  Therefore, a big investment in this kind of stuff would be rendered worthless by sudden prohibitive actions by the government.  This scares away that kind of big money.

Personally, I don't think FinCEN has yet abused its position, with regard to Bitcoin anyway.  But the possibility of it doing so is always going to be a variable.

I think the probability that Congress would do something insanely stupid if it did anything with regard to Bitcoin is a reason to prefer the current situation.  But that doesn't eliminate the downside of regulatory uncertainty.