canonically, humans and youkai must fight each other, and the spellcard rules were made so that youkai could fight the shrinemaiden without worrying about (the drawbacks of) defeating her. If Reimu were to retire, or become too grownup/elderly to play danmaku, she would need a successor (unless she's unavailable, for some reason), even if that successor doesn't get to appear in the games.
Marisa could've given less 'screen time' without much serious consequences, like Alice and Patchouli seem to be getting gradually less appearances, however Marisa could be also one of ZUN's ways of showing Gensokyo to the players, through the games, since Marisa is an human, and so, easier to identify with. (this isn't discrimination, it's said that youkai think differently from humans)
Maybe the challenge would be, to have another character that could be good enough to replace them. Possibly, a newcomer.