I've been playing this lately, and it's surprisingly good!
Though I'll be honest, the remake of 3 is definitely better than the remake for 2. The faithfulness of the music being the main reason. It makes the Genny sound chip really sing! The other reason is that 2 only has Japanese normal mode, not American normal mode.
Another change is that the buster in 1 and 2 is very weak against bosses, but isn't a problem in 3. Yellow Devil has slowdown in 1, so it's a little easier but the pattern is slightly different. On-screen items don't respawn in 1, meaning certain sections you need to beat in one go. A good change though is that if you are hit and fall on a spike in 1, you won't die immediately, so you can jump back up like in the other games.
Fighting the Dragon in 2 also requires you to stand on the middle block. And you also can't stop using the Time Stopper until it runs out, meaning you have to save it in Quickman's Stage until you get to use it on him.
Password system is gone, replaced by a save system.
I've only got through 1 and 2 so far, so I'll play the Wily's Tower once I beat 3. It seems interesting, but I'll need a guide for which items to choose.
For those that want to try it, download the Japanese rom since it's NTSC.