I think the main challenge the sequel will face, assuming that it will build on the foundation the 1st game has laid out, is enriching that preexisting base without harming its structure.
BotW is an ecosystem within which different elements work well with each other to provide a good experience. If you tweak a part, or add a new one, you might affect the rest of the architecture in unexpected ways.
The criticized weapon durability system, for example, incentivizes the player to explore to get new weapons, to try and get the optional chests in the shrines, or fight enemies with new weapons.
But it's also an incentive to come up with creative ways to deal with monsters when you don't want to use up your weapons or when they're all broken. It's an entry point to play and tug at other parts of the system - using the environment, special items or powers to do something innovative and rewarding.
Make weapons unbreakable or way more durable, and it's all these other ways of playing that lose a significant part of their appeal. The game is in a fragile yet sophisticated balance.
And that's just what could happen by trying to "fix" what's already there. Who's to say how adding radically new stuff, let's say a crafting system as a lot of people asked for, could affect the rest of the game and how it's played?
That's some fine tuning and planning that is required right there
The less risky enhancements they could bring definitely are incremental additions, that don't challenge the preexisting fundamentals but fit right in it.
That's the kind of things they can (and should) do relatively easily. Adding new mobs, new items, new natural resources, new recipes...
I'm glad they apparently do want to add radically new stuff though (floating islands, attachments to weaponry, new abilities). Wonder how they're going to balance it though
Like, the floating islands seem to fit right in Aonuma's vision of having to look in the distance to an objective, and figure out a way to get there (and that's genius in its own way), but how does that affect the climbing system already in place? Will climbing still be necessary like that with Link's new warping abilities (never used Revali's gale but it heard it was already detrimental to it)?
All of that aside, there are definitely some things that they could fix without harming the overall system:
- Animals despawning mid-chase