I finally found the time to do a build of the current git code of tomato for my RT-N16 and using 6to4 for IPv6 works really nice.
But I noticed that the inbound QOS rates I set for the different classes and also some of the classifications don't seem to work anymore.
It looks like the inbound limits are completely ignored and connections that come from the outside don't get classified anymore or get at most into the default class. This all worked nicely for weeks with build 54 and I'm using MAC adresses instead of IP adresses in the rules, so the QOS rules should be alright.
Turning IPv6 of doesn't help so it doesn't seem to be related to those changes.