I actually started with the PC-98 games.
Lotus Land Story and Mystic Square are probably the most accessible of the bunch being the most similar to the Windows era games. The hitboxes are bigger and I think the player in general moves faster, but other than that, they're the most accessible. They've still got a bit of unfair jank here and there. Shinki's cheeto bullets being able to kill you if the cheeto bullets in Yuki/Mai's fight were still on screen when you defeated one is the only one I can name of the top of my head though.
The Story of Eastern Wonderland has a lot of jank and... oddities... There's your hitbox being gigantic in general but also it being able to be offset if you get hit, some really unfair bullet patterns, NO focus mode at all, etc. (plus no joystick support in NP2 which was rather annoying for me...)
Phantasmagoria of Dimensional Dream and Highly Responsive to Prayers are both non-standard Touhou games
PoDD was sorta the "lets copy things from other things and see what we can make in it" game. There's traced art, stolen and non-credited graphics code, copied entire gameplay mechanics, etc. However I actually find it pretty fun while I was playing it and it had my entrypoint into the series in it (Strawberry Crisis).
HRtP is an odd game that I can not for the life of me play correctly. Maybe with a bit of polish it could be a really fun game, but in the state it's in now, not really.
The music for all the games (even HRtP) is still great though, if you like chiptune ^^
One day, im hoping that I can learn how to create a sorta N64/GC style version of the games and polish over a few oddities along the way, but that requires a monumental amount of effort and skill that i dont have lol