If you could remove a plot element/character from MEA what would it be, and what would you replace i

Kett. They did little to nothing to put themselves out as a major threat that needed dealing with. What the previous games did so well was that they made you invested in the villains. I didn't get that with the Kett.

Liam.

Irresponsible mutherfucker.

I really want to say the Kett because they failed as villains on so many levels, but I'm going to go with something else.

Vaults: Totally unnecessary, the go to a planet activate three vaults and raise the viability just got old quick. The game would have been much better off with each planet having its own unique issue stopping you from colonizing it. You could have discovered the Angarans on one planet, made first contact and then had to engage in some diplomacy, politics. You could have still had the situation on Kadara be another. A planet could have had a non-humanoid life form that was aggressive. Then you could have either found a way to compromise and co-exist or just gone straight conquerer and wiped them out.

But if you had to have vaults, you could have had one planet where the vault was malfunctioning and activated it. Which could have led you to look further into the tech and still lead you to the realization that the cluster was created by an advanced race who also created the Angarans.

But that's only if you absolutely had to have them for the story. I would have done away with them all together. Then the game could have focused more on you actually being a Pathfinder and not a vault activator as you would first on the ground on most of these planets ascertaining the situation and working to find a solution so you could start a colony.

Alec Ryder, or at least his death. Thanks to his face we had (probably) a very restrictive CC, plus he dies at mission N° 1, and there isn't even some kind of funeral or actually goodbye or a body.
I wasn't attached to him, I didn't have the chance to interact with him enought to be. Plus it was terribly clichè.

Remove all romance content, and instead give us a 90-second fully cinematic short of Grunt playing with dinosaur and spaceship action figures and making laser sounds with his mouth.

Remove the Kett and especially the Archon and replace them with something scarier and more urgent. If the villain suitably motivates me, I can more easily overlook other issues.

The ancient aliens plot hook. We've been there, done that. I realize that would probably mean retooling the motivations of all the factions in the game, but that would probably be for the best.

Remnant/vault gimmick. Press the button - fix a planet - repeat. Cheap, deus-exy (sorry for that word) and unrewarding. Not to mention a little detail - scourge supposedly broke these planets because it's attracted to remtech and we fix it by activating, that's right, remtech. What could possibly go wrong?
But that's the thing, they had personality. As you say yourself in next sentence this personality is pretty much there no matter what you do.

I chose the Kett not because we didn't need an antagonist, but said antagonist needed to be better. I've said it before. They're just Borg and their leader is a big babyhead emoji that broods. Oh, and we're supposed to believe that a ring fashioned in a circle out of his skullbone is natural and not machined on a lathe or otherwise carved. The list goes on with the Kett. If I could choose another thing, I'd say the corny firefly humor. I'm not saying eliminate levity, but the story was written seemingly by people who apparently have little experience in the world beyond working with other kids at gamestop.

remove the asari and replace them with quarians/drell/vorcha
remove the frozen mother popsicle and have father Ryder survive
remove the stowaway and replace her with no one
remove the tempest for a bigger ship so that the krogan doesn't have to be in the kitchen and the stowaway isn't with the escape pod
remove the car and replace it with a shuttle
remove Kosta and replace him with either Greer or Kirkland
remove Reyes and replace him with Zia
remove the implant for the sam voice thing and have the sam thing available through the omnitool
if Ryder doesn't let the krogan have the drive core, Ryder gets an option to put a 2nd outpost on Eos or Voeld
remove the angaran and replace them with a species know as the Unga Bunga. They have 4 arms, 3 legs and  3 eyes
remove Cora's commando dialogue and replace it with dialogue with her talking more about the alliance, gardening and sports especially football
when at the bar on Kadara for the first time, Ryder orders a Bud light and says "dilly, dilly" Everyone in the bar yells "DILLY, DILLY"
remove MEA and replace it with a sequel to ME3

The only thing I would remove is the open world design. But I'd improve some things, like the Kett would be more alien and much scarier.

I wouldn't change characters or plot, I don't expect to like all the characters in a game and I think disliking a character is as valid as liking them.

Remove every fetch quest from the game and replace them with more time spent on developing the world, the characters, the animation, and the plot. Aside from that, remove the Kett completely, rework the Angarans so they are more complex, spend the game either working with them to coexist or against them to conquer the cluster.