Final Level: Mission 6
Why It Sucked: So building an appropriately epic final boss battle isn't easy, but there is no way this was the best they could come up with. And after spending an entire game killing everything that moves, why would we suddenly decide that the hostile planet E.D.N. III "welcomes you like the warm bed of a lover"?
How We Would End It: Imagine if Mario had walked up to Bowser at the end of Super Mario 64 and slapped a GPS tracker on him so someone else could blow him up later. Than Wario shows up in a jet and they fly away into the sunset. Now pick anything else and it's a better ending.