Hear me out, i know it sounds crazy, but it would be guaranteed fun, As the name says a tower defence minigame, or not making it minigame and just another straight up game mode, it would be any of the iconic places in gensokyo (Let's say the Reimu Shrine) and then, tons of enemies come trough one or several already established paths, and, you can defend your Shrine with a character you have in your friend selection (Let's say you are defending with Flandre) and Flandre will attack using bullets, but the characters could also have the chance of using special abilities or spell cards, like, If Flandre is a destruction one then her special ability will be something like, clear a whole place out of enemies, or deal massive damage for several seconds.
The way you could only loose is if the enemies manage to go all the way trough to the end of the path (Let's say you have 10 lives) and if 10 enemies manage to go trough your defences you loose, and the only way of winning is if you defeat all enemies and manage to keep save the Shrine, clearly the final score is defined with how many lives the target had left.
And during the game, if a friend kills an enemy, that enemy will drop P points that you can use to upgrade the friend you want (Let's say the limit is level 5) and it could update their Damage, attack speed, or the power of their special ability etc, And i was also thinking if you left the points stacking you could call for some help, like some sort of button that costs 20 Points and if you press it the map will deal damage to all enemies present.
you could only choose 4 or 6 friends to bring to battle, and they divide according to their class (Heal, defence, debuff, attack) Heal types could not attack but instead giving a sort of boost to nearby friends, Defense types could work as some sort of human shield, place them in the middle of the path and the enemies will be distracted until they kill your friend, and the list goes on and on.