2 also has nonexistent weapon balance; stages that aren't completely accessible to the player from the start, creating some pseudo-linearity; disability to disable certain items at will; questionable enemy placement, level design, and spike placement; an obnoxiously long weapon get segment with mind-numbing music; and the BOOBEAM TRAP. Is the soundtrack good? Yes, definitely. Are the level's design themes fitting and inspired? Sure. Is that final segment before Alien Wily chilling and creepy? Totally. Is the game well-designed in general? Hell no.
I also really don't get how Megaman 2's weapons are more useful than... any other Megaman game. In 2, literally the only weapon I used apart from boss fights was the Metal Blade, whereas I use the weapons in the other games much more, and not at any required points. Honestly the only weapon you needed in 2 was Metal Blade, it ate up practically every enemy and could go in any direction without taking hardly any weapon energy, so why not stick to just it? Whereas in 3 I find myself switching up all the time, Magnet Missile to take care of pests difficult to aim at, Shadow Blade to one-hit kill the wasp enemy before it can drop its hive, Gemini Laser to take down some more powerful/annoying enemies in the way... Variety, the key to Megaman. Won't pretend they're all good, Top Spin is pretty stupid, but at least you get more use out of this arsenal than you do out of 2's.
Speaking of Top Man, I will admit his stage design is a little... odd, considering his theme, though we at least get enemies relevant to his theme. ... other than those cats. I still don't understand. As for Needle Man, let's be fair, how do you theme a stage after him? Spikes? It'd be smart if Wily actually did that but for the sake of game design, that'd be a boring level, lol. Plus, the robots are taking over the world, so why not have one terrorizing the town? Also, that stage has its own little clever design: You can see the giant Mettools (the hardhat enemy) under construction in the first visit, then in the second visit you actually fight them, which I thought was really awesome, personally. Speaking of the Doc Robot stages, I'm alright with them because the levels got their own tweaks so they weren't actually the same as the last time, though the 2 rematches... many of those were just evil.
I also thought 3 had better atmosphere anyway, because of Protoman and his mysteriousness. Story has never been Megaman's strong point, but the universe and lore definitely began to truly expand with this title.
That's how I feel, and part of why 3 will probably always be my favorite Megaman game. Admittedly in the end I may have to admit that 4 is a better-designed game overall, but 4 doesn't have the same atmosphere or godly soundtrack that 3 has. 6 does pretty well though.