Anime transformer ships? Hmm, how about anime battleships that transform into giant floating monkey heads with disembodied fists that punch at you and you have to hit them when the fists open up... and then once you destroy both hands the monkey inside says "Uncle Andross!" and blows up, and then the big surprise - that wasn't the end of the level, you still have to fight this giant bug thingy which shoots deadly radar beams out of its wings and sucks up rocks from the ground and flings them at you...
Darn it, I've been playing too much Starfox: Assault lately
Ever realize how Nintendo games seem to borrow from one another, though? Like there was Andross with the hand thing, and then in Mario 64 there are these giant stone hands which you have to punch (yes, the only Mario game where you can punch!) them when they open up, and then back to Oikonny in Starfox: Assault... and Metroid Prime's grapple beam was controlled in the exact same way you use Link's grappling hook in The Wind Waker... not to mention all the bosses where you have to reflect their attacks back at them (Aghanim from A Link to the Past, Ganon's first appearance in The Wind Waker, and every Kirby boss known to man)... yet for some reason you have to kill BOwser a different way every time?
Oh yeah, SE5... can we have weapons with multiple fire modes, like Megaman's M-Buster? One mode where it's really weak but fires like a machine gun and another mode where it's really powerful but you have to wait for it to charge? Just have a variable "time since last shot" and factor that into the damage calculation...