Donkey Kong Country 3 - I would expand it. Add more worlds, more secrets... Make it even better in exploration.

Super Metroid. - 2D to HD overhaul.

Ocarina of Time.
Not much because it’s basically perfect. But I’d add a sequence or dungeon before you awake as an adult, to actually earn the Light Medallion.

As for the poll, easily the 90s.

Yoshi's Island

Remove the balloon throwing minigame.
Tweak the triggers for the flying Shy Guys with red coins, as it's far too easy to miss some of them through no fault of your own.
Maybe add the feature from later games where you don't have to get everything in a single run to get 100 on a level.
Change More Monkey Madness and Kamek's Revenge a bit to make them less annoying.

RE4, and I struggle to think of anything I'd change, it's pretty much a perfect game in my view. 

From the poll, easily the 90s. It had both the golden age of 2D with SNES and Megadrive, the first exciting steps in 3D with N64/PS1/Saturn, and the Dreamcast to top it all off. 

So many of the best games ever made hail from this era; Ocarina of Time to Chrono Trigger to Super Mario World.

Technology was advancing at a lightning pace and every few months some revolutionary new game came out that redefined what was possible in the medium.

Ys 1. A Map to the cave and Dahm Tower.

I'd definitely get rid of the quick time events. That Krauser knife battle in particular is awful. I don't like Krauser in general, so I'd remove him, as well as one or two other bits from the Island section (e.g. those gauntlets of enemies right after your final battle with him where Mike helps you out in the chopper).

I loved the bit where you blast through the last of Saddler's forces with Mike's help personally. Great lead up to the finale.

I guess I wouldn't miss the QTEs that much, but I don't have any problem with them either, they weren't as forced or intrusive as in say RE5/6.

My favorites have always been Wing Commander 1&2.
If you play both with both expansions it's 110+ missions. In almost 100 of those you have exactly ONE wingman (except in WC1 they can die and leave you for mission or two without). There are few missions with extra wingmen, one way and another, to prove that was technically possible. But this was an element that was hardly at all used.

In fifth and final game Wing Commander Prophecy you always had two wingmen and usually another wing of three there to help, which changed the nature of the game.
I would've wanted one balanced game, with solo missions, most often one or two wingmen and some big battles. (I recall fan mod WC: Standoff did this pretty well.)

Oh ya, I'm planning to play the Steam version in the future, only played the SNES over a dozen times and the PS1 version once. 

Also have the game on iOS lol.

Oh ya, this one is a high up on the list - farming for the golden chocobo was a pain when I played the PC version - didnt bother doing it on the Switch version. 

Yeah the battles were really slow, at least on the modern versions, there is a speed boost option. 

But +10000000000 for the expanded character story arcs, a lot of missed potential. Hopefully the rumored remake takes advantage of that.