Boss patterns are identical. Room layouts are identical aside from Flash Man's refight. Hitbox differences are negligible and don't actually affect strategy. Altered weakness it is, I guess, but that doesn't really change how the fight plays out all that much. Still seems like a copy-and-paste job, and what's changed is not what's being pasted, but what it's being pasted into. That doesn't make it "new content" to me, it makes it "old content" in a "new game".
Patterns and room layout, yes. Hit-boxes and different weaknesses, plus other tools at your disposal (slide, weapons, Rush) make the fight different. A true "copy and paste" job would be if absolutely nothing changed. Slightly altered new-ness is still new whether you think it is or not.
Also, your question was how asking about the music reuse in MM9 was different than asking about the boss reuse in MM3. The fact that it had to be explained to you in the first place is kinda funny.
For fun, allow me to explain why I like MM3, despite my favorite character in the series being Blues. It's because MegaMan 3 continued the process of trying to improve upon the previous games.
-MM1 had only six RMs and the Magnet Beam.
-MM2 improved upon that by giving us 8 RMs and the Items, plus the secret "final" boss thingy.
-MM3 improved upon that by changing the Items into Rush, giving us the slide, Blues, and offering more to do besides just the Wily Castle. It also got rid of some of the immense "broken-ness" of the MM2 weaponry while also giving a slight homage to the previous game which, quite frankly, really is what gave the series its foothold in the video gaming world.
-MM4 improved upon that by giving us a whole new castle, altering Rush Jet so it's not so broken, adding in Fliptop and 2 other items, and last but not least, giving us the Mega Buster and an insanely better menu screen that the previous games.
Now here's where you can argue it goes slightly off track.
-MM5 gave us the improved Mega Buster, but it was so improved that there's no reason to use any of the other weapons in the game. Like...ever. Also, Beat was awesome.
-MM6 gave us the Rush Adapters, which were awesome, but the weapons were pretty bland and useless and again, really served little purpose because of the Mega Buster. The diverging pathways were cool though.
That's just the main classic NES games. The point I'm getting at is that MM3 really expanded on the already awesome MM2 formula and started to flesh out the series more than any other game. It's very similar to Link to the Past, in that regard. Did MM4 improve upon it? Yes. Yes it did. BECAUSE IT SHOULD HAVE! The goal always should be to improve upon the previous game. It's why Mega Man X was created in the first place, to improve upon the classic series which was starting to run out of ideas. Ultimately, the argument can be easily made that because of MM3, we have a lot of the MM games that we know and love today. MM3 is far from perfect, but the ideas presented in it helped to grow the franchise even further than it already did.
That is why I like it. It's not my favorite though. MM2 will always be my favorite because it was my first MM game. A lot of times, that's how it works.
Not as interested in changing minds as I am in encouraging critical thinking. "I like it cause I like it" doesn't really say anything, whereas actually thinking about aspects of design brings out more interesting discussion.
Critical thinking? How does "going back and forth about the same argument" and "how is my question about reusing music any different than reusing bosses?" qualify as critical thinking?