A big part of the problem was that the Supergirl part of the crossover was about 2 minutes of playing with portals, Flash spent its first third getting the plot back to that entry point before spending the rest of the episode on the fallout of noone having even the most rudimentary of basic tactical training, and most of Arrow consisted of a pointless dream sequence, thus leaving Legends to carry most of the weight which it doesn’t quite manage.
I don’t have any particular interest in the Arrowverse, but if there isn’t some sort of play given to the fact that their Earth has just had the existence of extraterrestial life confirmed in a less than benign manner, the people who do care should feel disappointed.
Some ways to make the incomprehensibly pointless inclusion of Supergirl in the CW crossover into a meaningful story choice:
1. Include at least some of the Supergirl supporting cast
Given the stakes, Kara should have brought at least Alex to Earth 1. Because Kara, enthusiastic puppy that she is, would still realise what her being stuck or killed there would have done to her sister, while Alex would never let Kara face that sort of danger alone. Given Legends as I understand it has basically made Canary banging someone every time the Waverider pulls over a running gag, giving her and Alex some scenes together where they can be queer and not in the story mutual love/lust interests would have been a brilliant thing. Or if Alex needs to stay because of Cadmus and her human dad, send Wynn along to be part of team tech support.
2. Kara dealing with her Zor-El angst
Instead of Felicity bugging Cisco about being nicer to the idiot who got his brother killed, picture it being Kara "I’ll always trust you Barry" Danvers who does it. Imagine if Cisco asked her "well how would you take it if someone you loved and looked up to did something stupid that threatened your entire world" and Kara draws a parallel between Flashpoint and her aunt's mind control or her father's genocide bug. Have the takeaway for Cisco and Kara be "we forgive because we have hope that our friends will do better next time, and because it's part of our own healing process". Instead of the whole "well I can't be angry because I fucked up the time lines like a complete boob too" stupidity jammed into the last episode of the crossover.
3. Making the climax even slightly heroic
Kara is familiar with the Dominators. Her universe’s version of them came to her Krypton and behaved exactly the same there as the Earth-1 Dominators are doing in the crossover.
It would have worked a hell of a lot better to have her be like "well we could give them Barry but in my universe at least they’re not known for upholding deals and very much are known for over reacting and invading places". Then it becomes an actual decision: "Do we risk Barry on the chance that they’ll go away" versus "Even though he's 100% willing we put the world at risk by refusing to extradite the actual person who fucked things up for everyone, just because we like him"?
Where did Kid Flash and the other speedster chick end up? If your resolution relies on superspeed delivery of macguffins across the globe, it's utterly criminal for the writers to elect to have the rookie no one wants in the field and the objector denying her powers not to be involved when the only alternative is oblivion.
If you're going to have Cisco vibe to the mother ship, have him port in the flatscans. Because if you're going to have the tech support faff around, it should have a meaningful result.
4. Everyone dealing more coherently with Meta angst
The repeating theme of the whole crossover was"what if metas do more harm than good", yeah? It was the entire reason the Dominators came to Earth, it was the message of everyone being pissed at Barry, it was the underlying purpose of the scene with the evil lady cyborg so Supergirl and Flash can prove they're the Good Ones and overcome that guy's senseless prejudice, it was the reason why Oliver was such a dick to Kara. So they chose to wasted almost an entire episode on completely ignoring that theme in favour of a navel gazing Black Mercy scenario.
The mind-control stuff however is very relevant. Everyone's angsting over metas being their own WMDs but nothing is said of the ramifications of someone else seizing control of them: As I understand it, Grod exists in the Arrowverse, and this is the second time Kara has almost killed people she cared about while under an external influence. But the writers never actually use it that way, it’s just a cheap excuse for a fight scene and then nobody even addresses it again. Instead of having Barry win the day, they could have used Red!Kara’s experience with J'onn, or with humans overcoming Myriad and working together to defeat kryptonians, to help show how metas aren’t an unbeatable trump card even when they go wrong. They could have had Barry and Kara talk about Flashpoint and Cat’s advice about learning as you go and regaining trust and how being more powerful means making bigger mistakes, but it also means the ability to do more to try to repair the damage afterward. What could be a better mirror for just how much damage Barry can cause, than a kryptonian under a yellow sun? How did they just completely ignore that? Imagine a scene for instance where Kara tries to talk to the Dominators on Earth’s behalf only to discover that although the Dominators exist in her reality, the Rao star system never gave rise to intelligent life in this one – or that they were responsible for the kryptonian genocide in both after discovering the whole yellow sun thing was actually the result of a metagene.