One big thing in my eyes?
Beyond all the issues about Schroedinger's Galactic Affairs or Time Skips or not saying what's going on in the galaxy, all of which people have mentioned for good reason, one of the big flaws is that it just made things too big, especially in KotFE.
The SWTOR engine is old, somewhat ailing and designed to do what it does. One character directly controlled, one character following along with AI controls, abilities to influence the world, stuff like that. It puts you into the action, which is nice, but it's not something designed for big epics.
The game makes the Outlander one of the most important people in the galaxy, and then has to try to justify reasons for them to head to the front lines to fight. Suspension of disbelief can take it to an extent, but it's a poor crutch to lean on, especially when it gets leaned on for every episode.
SWTOR has been a long, long history of making big, huge attempts at doing something amazing, coming a bit short or a lot short, and then spending the next few years paying for it.
The individual class stories? It means that every new story update with player voices has to bring back 16 voice actors just for one character's dialog. Also means that everyone's nostalgic for the class stories, when that creates a ton of work for not much gameplay content for the first run-through.
Nearly every quest fully voiced? Sets a precedent that makes quests introduced and completed only by text or one way conversations feel cheap instead of the routine.
SoR and Ziost? Rezzing the Emperor and showing his absurd power creates a character that simply cannot be fought in a conventional means, hence the Valkorion stuff to turn him into a threat that can be defeated in some manner.
KOTFE? Broke the status quo in a nigh-irreversible manner, requiring KOTET to rush in and try to get back to a new status quo as quickly as possible so they could tell other stories.
KOTET? Made the Outlander the most important person in the galaxy by giving them the Eternal Throne, compounding issues regarding telling a story with that character's importance.
They need to go small. Break up the Eternal Alliance, put the Outlander on the run or just not the most important person in the galaxy anymore and focus on telling smaller stories.
And hell, they have a course available. People care a fuck-ton more about what happened to Kira or Andronikous than they care about whatever BS is going on with Iokath. The small-scale spy/espionage/intrigue stuff has always been where the post-class-story content has worked best, focus on the characters because they're what we really care about now, just make some new, mysterious, maybe eldricht-ish threat that the Outlander goes off to deal with instead of playing galactic politics.