I've been using 6to4 ever since the 6bone shut down, and I've had no problems with it. In fact, it seems to me there are only two possible problems with 6to4 generally:
1. Bastard ISPs could, if they deeply inspect packets, see 6-in-4 packets generally as different or undesirable or whatever and do bad things like they do with bittorrent.
2. The 6to4 anycast default route as a mechanism to get from 6to4 space to the "real" IPv6 space can sometimes send your packets to a non-optimal gateway. The fix for this is simply for more such gateways to be created - preferably one (or more) per ISP - so that the traffic can be routed optimally.
I wanted to opt into Google over IPv6, but when I wrote them they told me to pound sand because I was using 6to4.