In the second season, Kompany should still be able to optimize their American profile to be able to defend the trophy. Yes, they did fail in the Champions League, but at least they have won the Bundesliga title.
On the other hand, Leverkusen will be left by Xabi next season, so they have to find another suitable coach, and this will be a challenge for their profile next season.
For Bayern you are right if Kompany stays for another season he could make their team even stronger in Germany and maybe help them to do better in Champions League because they will have learned from this season. It is also good for them to use their popularity in America to get more fans and make more money. Winning German league title is big deal and gives them good starting point for future.
But Leverkusen has big problem because their coach Xabi Alonso is leaving. They need to find another good coach who can keep team playing well and help players get better. This will be hard for them next season and could change how well they do in league. While Bayern may have stable coach in Kompany Leverkusen is going through time of change with their coaching staff which could make things uncertain for them.