The prominent reason why I'm part of the minority who adores PC-98 characters is because I like their designs. A lot. What can I say? I'm an artist. To me, outward appearance can easily be as much of a deciding factor on whether I'll like a character or not as their actual "character" - background, history, personality, what have you. A character's design plays a major part in first impression, and that's when you'll decide whether or not you're interested enough in this character that you would want to learn more about them, and as a result, like them more. I also find that "design" goes hand-in-hand with "character," meaning if I really like a character, I'll end up liking both of these aspects of that character, regardless of which one I started liking first. Of course, there are borderline cases. For example, I really do think that Sanae looks attractive, but I've never worked with the actual possibilities of her position as a character, and so, at this point, I'd consider her no more than eye candy (apologies to Sanae fans everywhere :ohdear:). But enough of that.
As far as Touhou goes, Marisa Kirisame was the first character that I can honestly say I've taken a liking to beyond just pretty pictures. Not only for how impressive her Master Spark is, but her overall attitude, occupation, and associated musical pieces. It didn't take me long, however, to start looking at the PC-98-era characters. Once I came across PoDD, a certain Yumemi Okazaki caught my attention. From there, she quickly overtook Marisa as my most favorite Touhou character (I'm not so sure how this happened myself, but I suspect part of it has to do with my soft spot for the PC-98 cast altogether). Almost a whole year has passed, and this position hasn't changed ever since. Despite the fandom being considerably more generous to the former in terms of exposure to fanworks, she still remains on top, while Marisa is still strong on second.
In the end, I don't think I can explain in detail why I truly like certain characters and not others. I could always say "I like her because I really like her design," or "her theme sounds awesome," but I know there'll always be something more to it.