If Ocarina of Time and Majora's Mask were rereleased on the Switch, I'd prefer if Nintendo redid the visuals again rather than simply converting the 3DS versions. As for gameplay changes, I think that Nintendo basically got it right for Ocarina of Time (about the only major change needed is making the Iron Boots equipped as an item), but they could do a lot better with Majora's Mask. The 3DS Majora's Mask seems to have a dumb or pointless change for every positive change it makes. Personally, I like the higher-resolution graphics and superior framerate, but I hate how every 3DS Majora's Mask boss has a giant eyeball weak point, which is a common Zelda boss trope that I've long been sick of.
In terms of performance, Nintendo can do a lot better than what they achieved on either the N64 (15-20 FPS) or the 3DS (30 FPS). These games are 20+ years old, and Nintendo should be able to release both of them at 60 FPS with enough tweaking.
I don't think I had any crashes during my last two playthroughs of the N64 version (which were on the Virtual Console, admittedly). Changing the Owl Statues into permanent saves was a pretty good change for the 3DS version, in my opinion, since it was on a handheld, but I am annoyed that Nintendo removed the option to save when turning back time to the first day. I don't get why the 3DS version couldn't have both the Song of Time and Owl Statues as saving options.