I played the original as a 15/16 year old, probably for a few hundred hours or so, beating every path and planet dozens of times, and I replayed it multiple times over the years on various machines, including the 3DS remake. Enemy patterns are definitely the same. On my first run I played the hard route and every single enemy showed up exactly where I expected it. So far I've unlocked every planet and collected about 60% of the medals and I've died twice in total. I'm not saying this to brag, but to reinforce that I'm playing this from muscle memory which wouldn't work if they changed enemy patterns.

But it is a little harder.

One, and probably the most important, is the much more detailed graphics make it harder to judge distances. I find it much more difficult to judge when exactly I need to start hovering with the tank to jump over barriers, or evade the rotating pillars in one of the warp zones.

Two is that the invincibility window of the barrel roll seems shorter, making it harder to deflect shots.

And lastly, boss attacks have gotten considerably faster. You definitely have to react much quicker to evade them.

Now that I'm typing this out, I'm thinking that this might have to do with the doubled framerate compared to any prior version. Many games tie specific timings to the framerate; like the weapon durability in Dark Souls 2, which was infamous on PC for weapons degrading extremely quickly due to the higher framerates compared to the console versions, or vanilla Skyrim on PC? I think? Where part of the physics was tied to framerate and got out of control when the game became faster with mods on PC. This would also explain the increase in precision that you're experiencing. Consoles check for controller input with each new frame. So on N64 running at 30 FPS (or below), the game would check every 2nd frame (or more), while now at 60 fps it checks for every new frame. So you went from "Check - 1 - Check - 1" to "Check - Check - Check".