Y'know, I was a 80% PC Gamer/20% PS2, but ever since I picked up an Xbox 360, I've barely touched my computer. Anyway, it's interesting that you mentioned Spider-man as having had better games -- I think some superheroes have powers that better lend themselves to standard controllers. For instance, any sort of shapeshifting superhero is hard to represent (or GL's ring powers).
I like what you said about secret identities, too. I know that some Spider-Man games have had Peter Parker missions which were usually photography based, but Clark Kent missions would be fun. I recently read Superman: Miracle Monday (which is how I found this site) and Chapter 13
https://www.supermanthroughtheages.com/thebook/mm/?chapter=13 shows Superman having to find a way to cover a series of disasters for the news as Kent while saving people as Superman. Brought over to gaming, that would be a neat trick to pull off.
As someone who also thinks about games, I think those game ideas are pretty good. I loved being invisible in Oblivion. If Portal makes any difference in gaming, I hope that it shows developers/producers that there is interest in shorter, inventive games. Not every game has to be a blockbuster.