So I have just finished a top run (all mission accomplished, true end)
My opinion is it lacks a few minor things, that there was no reason to change or update and one major gameplay issue.
For example theres no MISSON ACC-OMPLISHED *DUN DUN DUN* noise at the end with the text slamming in at each beat. Its tiny, small but theres no reason to remove it and just replaced it with just the text on screen. The original was much more impactful, so changing this to be... more boring is a choice.
Some cutscenes are just worse than the N64 original (I know amazing) for example in Sector Z you see the missiles come in and then light in the original accelerating towards the great fox, here there already on their way and they just maintain their speed, so it feels like a very static shot, again why change this to be worse?
Finally the big issue, enemy and bosses don't have any animation or sound effect when your hitting the right place, their just static until the health bar reaches zero and they explode. This is the worst change honestly and I hope it gets patched because it makes the entire game feel off, enemy's should respond to taking damage, it does not feel good to have zero feedback. It will be massively confusing to first time players.
But overall the update is great. I like the additional scenes, the remixed music and the graphics, but unless they fix the no reaction hits this makes the N64 version the best still. They fix that and I would say this is the better experience overall, but as is the N64 plays better due to that issue.