My favorite series of games in this "genre" if you can call it that is Fantasy Zone. They're very different from your typical shmup. You get dropped into a level and need to destroy a number of enemy spawners for the level's boss to spawn, collecting coins from defeated enemies to buy items, most of which are temporary, along the way.
I feel like a game like this would also be easier to make than your typical autoscrolling shmup because it relies less on scripting. That's scripting as in scripting levels, not programming ;)