I thought the crossover, overall, was very well done. They did a good job of having one storyline carry through all the shows, but each individual show still having their own point-of-view or "flavor" so to speak.
I think it was kind of a missed opportunity not to have the "kill all meta humans" weapon from the finale not tie into the "kill all aliens" weapon from Supergirl, given that they are so similar in concept and for the fact that it would have tied the Supergirl episode into the rest of the storyarc much better. Without that, the Supergirl episode remains almost an "after-credits" easter egg to launch the rest of the story.
I was impressed by what they achieved with the event overall, and I think the last 5 - 10 minutes of the finale were my favorite. (I don't know if this justifies spoiler text or not but I'll err on the side of caution.) Just seeing everyone hanging out in their civilian clothes and taking a moment to celebrate their win was really cool. It reminded me a little of the party scene from Avengers: Age of Ultron, which I also enjoyed. Something about seeing heroes in their downtime, just hanging out and being friends, I really enjoy that.