I really liked the old on-foot sections, but they were roughly 10x more enjoyable with the Wave Gun than without it. Without it was a nightmare, with it everything was incredibly easy. It was unforgiving enough in other aspects that I never felt like the Wave Gun was too much of an I Win button.

The frog in BMZ2 will teleport you back to the Gaia-Sophia even on the overworld! I only figured that out like 80% of the way through the game.