Let's take a look at the roster.
IaMP had, IIRC:
Reimu, Marisa, Alice, Patchouli, Sakuya, Youmu, Remilia, Suika, Yuyuko, and Yukari. Plus Meiling, though she didn't have a story mode.
Reimu and Marisa can be crossed off because they're the main protagonists of the series.
At the time the game was released (following IN, I believe), Sakuya had been in the previous three games, twice as a playable character, so we can cross her off.
Suika was new, so cross her off.
Meiling belongs in a fighting game, 'nuff said.
Now we have Alice, Patchouli, Youmu, Remilia, Yuyuko, and Yukari. Here things get a bit less clear cut.
I'd say Youmu belongs in a fighting game too, and the rest are there because, having links to characters already in the roster, they have more of a reason to be there than, say, Rumia or Letty.
Patchouli, Remilia, and Yukari also have reasons to be in the game because they're related to Suika in one way or another.
You could also argue they just included all the previously playable characters first, (Reimu, Marisa, Sakuya, Yukari, Alice, Remilia, Youmu and Yuyuko), added Suika as a new boss, and threw in Meiling for fightyness and Patchouli to finish the SDM crew (sans Flandre, who I believe is fairly popular, and thus should've been included if IaMP was meant to be an all-star roster).
SWR had the same roster plus a few additions. We can cross off all the above because they were already in the previous game, and replacing them would be more jarring than leaving them in.
Iku and Tenshi are new, and Aya lives on the mountain half the characters have to climb up, obvious choice. Momiji would've almost certainly been there too if she'd been a boss instead of a midboss.
I can't think of a reason Reisen or Komachi would be there off the top of my head (other than to put in a character from IN and PoFV, and the whole shinigami-celestial thing), but then, I've never seen any indication that they're particularly popular either.
