True. Having an open-mind is important to uncover interesting character integration. In another post, someone wanted to make a fan-game with Mike, but people weren't interested because that character doesn't have much going on officially so it was "shut down". Depending on the game idea, it could have worked (like, we know she want to sell cards to the player, so she might be a merchant. Or maybe she just like making money and use the cards as an opportunity. Either way, you can make a game where you have to handle her shop).
You have to be careful though to not mix what's in the official games (which often leave some gaps), and your imagination of a character. For instance: Elly. Officially, she's just another "guardian" that's get beaten by both Reimu and Marisa, and there's no connection between her and Yuuka other than they are in the same world. Imagination is fine, but not everyone will imagine the same amount of depth for character like these that get very little screentime. Worse, some people may imagine negative things about a character. There's a reason why characters that appear often, and therefor usually better defined (like Aya that has 2 spin-off games, playable in 2 main-line, and appear a lot in print works due to her being a tengu and a news-writer), are generally popular. You can't really blame people for choosing whichever character left a bigger impression on them (and having a character returns multiple time is of good way of doing that, like Mima did during the PC98 games) and not giving as much attention to a lesser-defined character that could be interesting with a bit of imagination when there's +100 more characters in the series. Maybe for those who have been in the community for a long time it's different and they are tired of seeing the same character over and over in fan-works.
Here's what I remember about both Elly and Mima without doing any research, as well as quick stuff I can imagine from that:
Elly: She's a guardian. Has a scythe so maybe(?) is related to death. Live's in Mugekkan (sorry for spelling) or maybe (?) between Gensokyo and Mugekkan , so maybe (?) connected to Yuuka. Was beaten / let slip Reimu/Marisa, so maybe (?) clumsy
Mima: She's a vengeful spirit (can imagine various relations with the other spirits, as well as her having the ability to posses someone). She was sealed (can imagine it was by Reimu or the previous Shrine Maiden. Can imagine she has a grudge against the Hakurei familly, or maybe her grudge is something else), but breaks free then fights against Reimu, but then becomes somewhat friend in the ending of MS (much like other Yokai in windows game). She's stronger at night (can imagine she's somehow related to the moon). She often lies and is mean to other people, making fun of them without losing her cool. She teached Marisa magic (can imagine many thing of that).
For me, it's easier to see Mima as a more relevant character than Elly given how many official stuff she has going for, and this it turns makes it easier for me to imagine various scenario involving Mima. It could be different for you. I picked Elly as a mere example.
Btw, I sort-of written my previous message as "If I had to pick only ONE character to represent PC98, who would I pick" (forgot to actually mention it though). I don't want to turn this post into "Mima's good, actually", just that there is some merit behind Mima being one of the more popular PC98 character (other than the meme, of course)