You will need to adjust your team for the boss you're going to face, sounds like good game design for a tower defense imo. Would be pretty boring if the same comp you used to steamroll 99 waves would kill the boss too.
Thank you for this gem! For the future: i would really like to see more area-buffing pokemon like farfetch'd and sunflora but with stats like crit rate and recharge time. Keep up the good work!