I was disappointed by Neutopia II. I love the first game and have been meaning to give the sequel another shot, but it just wasn't as fun or special. Like Bomberman '94, it seemed to be a case of throwing a bunch more stuff into a sequel without narrowing down the magic that made the previous game so timeless.
Having played both at approximately the same time, I have a different view. Neutopia 2 just improved on so much of the first one.
First, the Moonbeam moss mechanic was absolutely obnoxious in the first one - every 6 rooms you have to pause, switch to the MBM, and re-light, then switch back to your other item. Irritating! I believe it lasts longer in N2, and faaaar less rooms use the lights-out mechanic.
Second, you don't get the speed-boots until the 4th plateau in Neutopia, 6 dungeons in. So it is sloooow walking for 3/4 of the game. In N2, you get them after the 3rd dungeon, which means you get them 3/8ths of the way through - much better.
Story wise, there is a reason to go through each dungeon in N2. Get the MacGuffin to get around the next hurdle, which is at least slightly more interesting then "Collect 8 MacGuffin's in order, because we said so."
Finally, the boss fights in N2 are just far, far more interesting. I feel like N1 the bosses were just sorta "Welp, we need a boss, what is the most generic thing we can think of?" N2 had far more interesting battles.
That said, I can see where N2 is just N1 plus a few improvements - filtered through the glasses of nostalgia, it would seem better than a mediocre sequel.
