I think this suggestion is reasonable but may make the game a little more complicate.

If Nordeus don't mind making the game complicate, I also suggest that league with teams strongly performed in Champion League (not Cup) may be assigned with more quota to participate Champion League in next season.

I think it is fair. Champion League is mainly participated by teams in same level and with different qualities. So performance in this competition reflect relative qualities of teams and in turn the league they are participating. This is also similar to real world European champion league.