I have a really nasty feeling what they're going to do is make MM a lot easier than the N64 version. That's my argument against more time travel flexibility and things like that- kids these days should have to suffer as we did!! No, in all honesty, I think they need to change the save system because it was the MM save system that always screwed me over, personally, especially when you can't always complete what you're doing before you have to stop playing for some reason. That's the only change I really want to see. What I don't want to see, is like what they did in OoT-3DS with the Water Temple, where they colour coded the doors and things like that. I know that was a hard dungeon but now people get confused when us old N64 lags talk about that dungeon being hard because they had the easy way out. I guess it's a bit of nostalgia mixing with bitterness, but I don't genuinely believe that major alterations need to be made to the gameplay, just maybe a few tweaks here and there given the capacity the 3DS has in comparison to the N64, which couldn't even hold MM and you needed the expansion pak for it. Idk.
End of rambling on, I'm not sure about MQ. I don't really think it needs it, this game is already hard. Perhaps make the overworld more accessible in some way? Just in the sense I never got the feeling I could really explore Termina outside of the storyline without triggering a quest I didn't want to do yet or something. Perhaps one way would be to make it so that if you miss something or don't want to do a particulat sidequest yet, it doesn't mess you up in between dungeons. Like, not to make them completely skippable but... I'm explaining this badly.