Needs more men
why does this sentence reminds me of Valis IV? (I'm yet to play the non-SNES version :p)
Well, I must admit that I haven't thought well enough about a game having multiple final bosses (even if IN managed to do that), since there must be someone to start an... incident!!! (haven't played any VN games, so I don't know if this idea of possible different final bosses could still work :p)
Also, I would like the games to not have graze amount as one of the most important elements in scoring (can be a secondary element, though, or perhaps yield more points when attacking while or after grazing, for a short time; I liked the gauge in SA); there are other elements such as bullet cancels (Progear, ESP Galuda, Dodonpachi -- in this example, certain enemies clear the bullets on the screen when destroyed), chain hits (Dodonpachi, Mushihimesama -- in this example, it's fun to see the counter going up, but it's a bit troublesome to do so optimally) and usage of resources (Cyvern and Armed Police Batrider, to not mention ESP Galuda -- in Cyvern, you have the Banish meter, you must use it wisely and collect Banish refill items strategically; in APB, bombs often yield more points than normal/option shots and may have a larger coverage depending on the ship, besides being used to destroy background elements for points and revealing point medals that can't be attained otherwise; both games also feature medal upgrade systems, that increase the value of medals collected); there might be other ways, or ways to adapt these into Touhou :p