I love a ton of these ideas! I especially like the Dev commentary, Episode Metal and alternate Zone paths leading into new Zones- the last one reminds me a bit of Star Fox and how you can trigger an alternate final level by destroying the wrong asteroid and being sent into a totally different area and "final" boss.
And on the Dev note... I would love to see Dev ghosts for each of the Time Attacks!! It's nice to actually see a result you wanna beat out, and would give Time Attack a little more life.
I know, probably simple ideas myself~ But after trying Marathon Mode and seeing what it has to offer... I'd personally like to see Challenge Runs! Same structure as Marathon Mode, you dive in the full game with 1 life, but you have restrictions placed on you or alterations. A "Hard" mode already exists with Ultimate Mode... but lets get crazy.
How about... Super Mode, where you play as Super Sonic- but you have to tangle with altered levels designed specifically to challenge, drain and outright kill Super? Maybe a Combo Mode, where you're tasked with keeping up an badnik/monitor destruction count for a massive score boost? Let's go even further with a new run for just Fang, where you get better damage VS bosses for long range and/or trick shots? Or something as simple as a Boss Rus- oh, that got made already.
I really like threads like these as they get the creative juices flowing. Wonder what will come next?