For instance in some games it might not be necessary to save a reference to a targeted object, if the gameplay targeting mechanism picks up a target in the first frame after loading a savegame anyway (etc etc...). Whether that target is exactly the same as at the time of creating the savegame might not be relevant (but very relevant for other games).

I guess the TL;DR is: in many cases it might be much easier to come up with a specialized per-game savegame system instead of coming up with a generic savegame system that works for all types of games.