[@mattmanganon]

So for those who were absorbed, you can use them in their pre-marvel states.  Just pretend they never crossed over into Marvel territory.

As for those characters that passed around like the roast turkey on Thanksgiving Day, try to avoid Marvel/DC versions as much as possible, maybe take a certain aspect or idea if you want but they shouldn't be that version of them.

I feel it's kind of a case by case basis for those rights nightmare scenarios.  I think it mostly comes down to if they are too ingrained in the bigger Marvelverse, or if they have their own universes and are just owned by Marvel.  Like I think Transformers has enough of its own universe and story to easily make the transition without bringing any Marvelverse aspects with it.