The heroes of a defeated faction not just disappearing would be nice. All of them going up for sale on the market place would the most basic solution, but it might be more interesting to add some other options. Like some heroes joining any faction but ones that just killed them (out of spite or rage). Or returning to their home faction, with hero’s from minor factions been attainable when the corresponding minor faction is obtained or (if the minor faction has been absorbed by a major faction) that major faction.

As for replacing the generic skill tree… I think it’s there as a way to guaranty some functionally of a hero no matter what, it’s also nice to know that they will definitely have *at least these* skills. Plus, some of them are good, like the xp per turn on fleets and the extra approval can be nice. However, I get what you're sating- modifying some of them based on your faction could be interesting.