I've decided to make a short list (that I want people to add to FOR THE LOVE OF GOD PLEASE ADD TO THIS LIST) of things that every Ocarina of Time, Majora's Mask, Wind Waker, etc in 2d has done wrong, and ways to solve the problem. It's more of a uh... what to avoid sort of thing, since we've had a new OoT2d crop up yearly here or there by somebody, either in public or private. Please note, this list is just kind of overall observances- of course there are ways to do these things properly. This just observes how they don't fit. These are just things I feel devs get hung up on when trying to make a 2d remake. Focus is on Ocarina of Time.
Identifying why Certain Mechanics Exist
This is important. A lot of times people try to justify having elements in their 2d versions that only exist to progress the 3d version in a way that makes sense only to that version. Don't be afraid to rework things to make sense for your version of the game. This is the basis behind each item in this list, especially the next one.
Trying to Make a 1:1 Conversion from 3d to 2d
This... Isn't possible. You have to make necessary changes and adaptations. Sometimes outright, completely different chunks and mechanics to the games to make it work. A good example is Z targeting in a Link to the Past or Link's Awakening style game. Some plotlines might need to be adapted to make things work.
Epona may work for ALttP, however in GB games (with a small screen and room size), it doesn't make sense to have her at all. Moosh and that other thing from the OoA/S games worked because they weren't fast travel- instead, they offered new mechanics to progress. Epona doesn't offer much in the way of progression in a 2d lttp/LA environment with the exception of crossing into Gerudo Valley, but even then- you can find other ways to allow the player to cross that bridge without her. Replace the race to get her with an Ingo milk drinking competition or something, and give Link a goddamned Roc's Feather.
Often developers will try to make a huge 1:1 overworld. The problem with this is you end up with a lot of unimportant space. There's no real scope from the top down perspective. In Ocarina of Time, you could see things in the distance; know how far you had to go. Not every part of the map had to serve a purpose. In LA or ALttP style, 80% of the rooms on the map serve some form of purpose, or convey progression. A giant over world would feel boring. I feel the trick would be to condense the overworld portions, and rearrange some side quest elements through it to give it more importance.
Trying to Find a Place for EVERY NPC
This just can't work. Kokiri Forest for example has a LOT of NPCs that simply tell you about game mechanics that shouldn't exist in 2d. They could either be removed, or repurposed with different dialog- but keeping the same dialog or trying to replicate the mechanics that don't translate well would be a mistake.
The Adult/Child Link Conundrum
This is one thing that's always bothered me. For aLttP you *can* have an adult link, but he always looks very strange. Link's Awakening however, there's no way to have an adult link. How do you solve this? Well simple- Think of Adult Link Hyrule as a new map; like the Dark World. There are differences in it that allow you to progress certain places you couldn't before. There's no need for crawly holes because in the future they could just simply *not be there*.
So Many Items
The core items are nice, and they make sense. There are some however... that don't need to be brought over. This isn't necessarily a problem with 3d to 2d, but it's a general observation. Bottles for example don't need to exist in a GB port. There are ways to tighten up the item load and eliminate some additional event threads that have a harder time existing in 2d (planting those damned floaty plants for example in OoT). Things like the hover boots are a bit strange, because they can be used, but then the Iron Boots don't really fit in aLttP style. In LA style you could use the iron boots for platformer underwater segments easy. Even then, you can probably figure something out around this whole mechanic.
Making Ledges you Jump Across
No. No no no. Come up with another mechanic that works in 2d. This always feels gross and terrible. It's barely necessary in 3d. In Link's Awakening, there would be a switch to press that extends a bridge if it's 100% necessary to cross.
Ignoring the Established Mechanics of the Style you're Working With
This is the final, probably most important thing. If something doesn't fit in the world you're trying to cram the conversion into, you shouldn't do it. Come up with a more unique way to convey what they tried to convey in 3d. Make something that works for 2d. It can be completely new, or borrowed from the style of game you are working from, but don't take from the 3d version if it's something meant for 3d. Again, those little floaty plants are the best example. You're better off making them create holes in the ground with new grottos to give you the item they'd lead to.