Having played the entire game from start to finish I don't disagree with Jaffe here and I think that Miyamoto would've made big changes to the beginning of the game and the map screen.
Dread is presented and starts as a sequel to Metroid Fusion as if you've picked it up a year later but it has been 2 decades since Fusion released and 5 years since Samus Returns dropped.
At some point they give you an item which is sort of like a cheat to scan rooms but that's only near the end.
It's a great game but the balance and structure is so weird and off. As if they had to overhaul and rearrange the whole thing mid development because the level design didn't work out.
I mean Nintendo really isnt into remasters as much as repackaging their old games with barebones effort and charging maximum price
Nintendo does remakes well (The Wind Waker HD, Samus Returns, Fire Emblem Echoes, Link's Awakening HD) but they don't do them often because they take away resources from developing new games and seldom sell as well as new entries.
Remasters are a mixed bag, some have been great like Xenoblade DE others just sort of emulated ports.
A sort of middle ground between the remake and remaster like Nightdive Studios is doing with their games would certainly work for Nintendo 64 classics.
However, I can't see Nintendo hand the big guns like OOT to them or make the return of F-Zero, Star Fox 64 or WaveRace happen with a sort-of remaster.