I agree with your points on Death Egg to a degree. The problem is that Tails will follow you when Sky Sanctuary collapses and you jump for Death Egg. If you're going to keep Tails back, then you really need to have Tails part company with Sonic before the fight with Metal Sonic. You could even have Tails in the tornado flying in the background whilst you fight Metal Sonic just to set the idea. It's not how S3K had it, but it makes more sense than how it actually played out. I also think for continuity, Tails should stick with Sonic at the end of Launch Base, purely because of how Mushroom Hill starts. Also consider disabling Hyper Sonic after Robotnik steals the Master Emerald.