Emulator

Android already does that IIRC.

Exactly what you describe in suggestion 3 is already implemented in Dolphin since a long time ago. This makes the confirmation dialog with a warning that you describe in suggestion 1 unnecessary - if the savestate format version is different, we already know that trying to load the savestate will end up breaking everything because things are in the wrong places, so let's not offer the user the option to try loading it.

Furthermore, when it comes to suggestion 1: Highlighting games with autosaves is rather pointless, because if you have autosaves turned on, every game you've played will be highlighted (and I'm going to assume that users won't switch autosaves on and off all the time for different games, because then they might as well just make savestates manually without losing time). Besides, just highlighting them won't explain to users that they need to make proper saves prior to updating. We need to write a text about it somewhere, but is it really possible for us to make it show up in a place/way so that users actually will care about it and not forget? And there's an even bigger problem that hasn't been addressed: One of the most commonly reported problems with savestates is that making normal saves sometimes becomes impossible after using savestates too much!

Not automatically loading incompatible save states but keeping them on the disk (suggestion 2) makes perfect sense, but it's a more or less obvious thing to implement considering that we already can detect incompatible savestates.

If the intended use case is when the user hasn't reached a proper save point, this feature will only be useful sometimes. I think it would be better if the user has to take the few seconds to make savestates manually in those cases rather than ending up using savestates even when they don't need to because Dolphin "conveniently" does it for them automatically and they don't know any better. There are many people who don't know how saving works and won't question something that makes booting games quicker.

Anyway, the savestate instability problems are more problematic than version incompatibilities. If the user updates Dolphin and savestates don't work, they can go back to the old version. If savestates randomly don't work and the user hasn't made regular saves, they've lost all their game progress. As long as that's not solved, we should be very very careful with implementing automatic savestates.