Homunculus Origins - This one has gotten praise from the author of the manga and it wasn't all bad, and was an interesting take on them so this may not get a lot of votes. What bugged me about it is, if human transmutation was attempted an EIGHTH time, what would the next Homunculus be called? Since they are clearly named for the Seven Deadly Sins (which makes more sense in Brotherhood) but once all those names are taken, then what?

Its villain - Father was a better villain than Dante, and plus Dante being a twist villain meant that she didn't have much presence as the villain of the series. Her defeat isn't really that clear until the movie where Gluttony turns up alive and she doesn't.

Filler episodes - This has my vote. Some of them were so boring, it's no wonder they decided to split off from the main story and tell their own version of it since they were clearly having difficulty waiting for the manga to tell its next chapter. I thought I really liked FMA when I first saw it, but after I saw Brotherhood, I realized how inferior original FMA was, and I demoted it harshly on my list.

Entering "our world" - I really don't think this was necessary, especially for a fantasy world like FMA. That world is so much less fun, and most of the movie - which is required for closure with the last three Homunculi, especially Envy - is set in it. This NEARLY got my vote.

Adaptational Villainy - Hohenheim was basically the Gandalf or Dumbledore of Brotherhood, but while an ally to his sons in FMA, he was once Dante's partner who took part in her actions. Basque Grand was also not evil in FMA, but in Brotherhood, he was super corrupt and was even the one responsible for Winry's parents' deaths (though he didn't do it himself if I recall).

As someone who prefers the 2003 anime over Brotherhood significantly, I think my main issue with 2003 is that they made Archer a terminator. Not only does it look ridiculous and feel completely out of place, but then he gets killed with a regular pistol despite being a huge monstrous cyborg thing. I can excuse a lot of flaws in FMA/manga/Brotherhood, but cyborg terminators is where I draw the line lol.

Also, on the villains, I've never understand people thinking Father is a better villain personally...Dante could've used more screentime, yeah, but her plan of instigating mass slaughters to create Philosopher's Stones is a lot more interesting to me than Father's ultimate goal of 'become God' which is done in tons of media already. Also his plan is super haphazardly put together, he's had YEARS to find sacrifices, but then he lets them all wander freely instead of keeping them captive until the Promised Day, and ends up scrambling at the end because they literally didn't have enough sacrifices. If any of his sacrifices (Edward, Alphonse, Izumi) left Amestris he would've been completely screwed when the Promised Day finally came. It makes Father seem really sloppy and careless. He left everything up to chance and rarely took initiative.

Father also has so much more screentime than Dante, but feels so much more boring. He got an interesting backstory but then spends 90% of his time just chilling underground letting everyone else do the work. Dante actually did things herself, not just leaving it all to the Homunculi, like when she went to Liore to manipulate Rose. Also since you don't know Dante stole Lyra's body on your first watch, a lot of scenes take new meaning when you rewatch the show knowing Lyra has been dead this whole time.

I also never really liked the climax of Father becoming this absurdly huge monster (which itself feels really out of place in FMA), everyone is basically dead without their souls...then it all gets undone in literal minutes. Really underwhelming. The final confrontation between Dante/Envy and Edward was a lot more straightforward, which I like better.

Then again 2003 got a second "final battle" in the movie with Eckhart, which is pretty much just flashy alchemy with no substance with a super boring villain...so I guess it kinda balances out.

I should clarify--I don't think Father is a BAD villain. But he's also not objectively better than Dante. They both have things I think could've been done better.

That did bug me a bit too, Archer getting shot in the back despite his whole cyborg thing, at first I wasn't even 100% sure that he was dead.

Yeah, he reaalllyy should've just died when Scar made his sacrifice. Would've been a much more fitting end to Archer than having him survive to become a literal cyborg...