100%'d the game N64 style, 7 cycles. That is to say, I didn't find the 7th bottle. All I know is that it involves the gorman brothers but when I'm cramming so much stuff into each cycle spending time looking around to find this bottle is kind of hard. I could have probably done it in 6 cycles though; I had a few mess-ups due to forgotten times for when events triggered (missed the bomb thieving like 3 times) and I took too long in Snowhead to be able to save Romani on the same cycle.
Overall I didn't get bothered by the changes as much as I was worried I would. I still don't approve of the save change but it doesn't affect me much anyway as a MM veteran; I only ever saved when I found new statues and at the start of every cycle anyway. Never used a feather statue, though I did reset once or twice just to check how long certain events would take. The only thing which I couldn't get over was the swimming change, and even worse, the huge lack of magic scattered around Great Bay to make up for the dumb change. I was pretty much devoid of magic for the entirety of my time doing story objectives in Great Bay and it was annoying as hell. It was great when I finally got the Chateau Romani, which I then used ASAP every cycle after to avoid having to deal with the terrible swimming altogether. That definitely slowed down that specific cycle by a lot.
As for the bosses
(spoilers, obviously):
Goht: I don't mind his changes much because it's pretty much the same fight. I can't say it's any worse, but I do still prefer the original because the feeling of rolling into Goht repeatedly when you knock it down was really satisfying in the originals, but can't be done in the remake.
Gyorg: Not that bad, but annoying. The first phase is okay but gets boring quickly without having to jump in to damage it. The second phase is just a ton of waiting for the boss to line itself up with the bombs so you can damage it. I don't mind the concept of the fight, I just hate the waiting. A downgrade from the original.
Twinmold: I like what they were going for here but hate the execution. Fighting the blue worm is okay but I feel like there should have been another step to damage it. As it is I can kill the blue worm without ever moving. This part of the fight reminded me a lot of Phalanx from Shadow of the Colossus, so it might have been cool if you climbed on top of it when it was down then used the Giants Mask to weigh it down and crush it or something like that. Fighting the red worm sucks. The fight is waaaaaaaaaaaaay too fucking long and your attacks as a giant aren't very accurate. I constantly felt like I was hitting his spawns but missed most of the time. I like how you can roll over those things though. I also had a pretty good laugh seeing Link spin the worm around and slam it on the ground, followed by a "HAAAA!" But after the first 2 hits they give to you it takes way too long and gets dull really quick.
Unfortunately with the boss changes the devs seem to forget that the player is on a timer. They don't have all the time in the world to dispatch a boss. Except for Goht, all the bosses were changed to be much longer, even if you know what you're doing, and that just doesn't work in MM. They also all involve a lot of waiting (again, except for Goht), which is equally annoying. In the original, boss fights moved as fast you were able to make them move, but in MM3D they're always slow unless the RNG is on your side.