Miners that refuse to include transactions are becoming a problem
and the posts expressing concerns about Vlad's ASIC operation,
[ANN] A public company will build a huge Bitcoin Mining Operation (ASIC).
It seems there are a lot of people who still think this is a subject to worry about.
Mystery Miner was likely a botnet owner (perhaps targeting Macs) that appears to be gone now. Nevertheless, developers started to think about ways to assure the work for a block will actually be done. So, this issue doesn't seem to be a great concern right now.
I believe many problems are solvable because Bitcoin is a dynamic system in many ways. Users, miners, pool operators, future Asic farmers, developers and many more all have the ability to act upon upcoming problems. Vlad's plans are still plans only and he will not be the only one coming up with Asics. It's the way things work in technology. There'll always be a bigger fish. Just because he says so doesn't give him any advantage over other competitors and we will see what will happen in the perhaps not so distant future.
Another worry of mine was the entire "tainted coins" issue with MtGox acting as a self-proclaimed law enforcement agency. This will also not likely to be be a fatal problem. Either Gox will really hurt its reputation and lose a lot of money and/or people will start mixing coins all over the place (happens anway in time).
Personally, although I'm convinced Bitcoin is a great project remember not to invest more than you can afford to lose. It is risky. Shit may still hit the fan, as they say. (Don't ask me who they are.)
It's good risks are being discussed to find out if they really are a problem or not.