If they want to maintain their performance next season then Leverkusen should try to add depth to their squad because they will be playing in the Champions League. The decision to stay is much better than leaving too quickly to take charge of another team because Xabi Alonso needs to prove his quality as a coach. Playing in the Champions League will mean that Xabi needs several quality players because the matches there will be much different from the Bundesliga.
Next season will be a real challenge for Leverkusen. They will play in the Champions League and that is a high level competition. Xabi must be able to rotate players and add variations to match tactics. I think club management will give Xabi a budget to find the players he wants. And for tactics I think if you play at a level like the Champions League you really need a variety of tactics because strong teams from other leagues will look for your weaknesses. And if they find your weaknesses then the teams in the domestic league will also find out your tactical weaknesses if you lack tactics.
The next challenge is that Bayern Munich will be better prepared for Leverkusen. I'm sure this season they really didn't expect Leverkusen to be a problem for them. And they definitely won't let that happen again next season.
I also buys into your sentiment about Bayern Leverkusen, because since they will be playing in Europe most prestigious competition, the uefa champions league next season, they will definitely face a much stronger test than they have face throughout this season, and in other for them to to be able to cope with the pressure of expectations, they definitely have to strengthen their squad.
And as for Bayern Munich, if Bayern Munich do not improve massively next season, they would still struggle next season, unless their is a big changes within the team that makes the team to be much better than this season, if not, Bayern Leverkusen will still dominate them, because I believe that Leverkusen is their to stay, as long as xabi Alonso is still their manager.