Try moving your Layer-7 filter rule at bottom of chain, and do some optimization of firewall filter rules. Looks like your firewall is culprit here.
It would help a lot to track issue if you post screenshot of tools->profile.

Is there any timeline for IPv6 route marking? or Is it still impossible to implement on routeros6 due to kernel limitations?

It is not never. I suggested to stop worrying about it and use v6. About the features, which features do you need? Remember that MikroTik does not implement features by demand. It might not be feasible or possible to make something. Everything has to be evaluated individually. About features, due t...