Labyrinth of Touhou and Genius of sappheiros are amazing rpgs in their own right that blow most commercial ones out of the water in terms of strategic depth and replayability IMO.
Mystical chain is a really fun game. It's about as long as a regular touhou game, but its playstyle is more like..umm.. some kinda single player adventure version of super smash bros? It's kinda hard to explain. Just watch some youtube vids of it, they capture the gameplay pretty well, and are pretty fun to watch.
I know you said no danmakufu, but I dunno why. Maybe you only enjoy them to be full games instead of individual stages or minigames? If so I really like phantasm romance. Its danmaku is even prettier than the official games IMO, though the music is nowhere near as good.
Everyone else seems to prefer concealed to conclusion though, so you may wanna try that instead if you're open to trying anything at all. I didn't think it was as fun though personally.
I still haven't gotten around to trying that Youmu Ys game, derp.
Also if you like pokemon (I never tried it), Touhoumon is supposedly amazing, I dunno.