I like to have some sort of "climax" to the level. So, I'd like a boss in each stage.
However, I'd prefer it done like Banjo-Tooie and not Donkey Kong 64. I'd like the boss to be organically in the stage, rather than accessed by a portal. Then again, if you can make it work similarly to Donkey Kong 64, but having a more organic arena without using portals, that would be fine, too.