'Hank and Dawn' should have come earlier (the weird scenes with Rachel reaching out would have still worked, albeit in a timey wimey way).
Then the Finale, whilst an interesting 'Elseworlds' story, completely killed any momentum the main plot had going. I wasn't wanting resolution to the Trigon storyline, but it could have been progressed a bit further and still led to a decent cliffhanger.
That said, some good scenes before, and then in, Gotham. Just the right amount of Batman and they made him plausibly terrifying, particularly in the aftermath at Arkham and then the final scenes in the Batcave.
Knowing it was all an induced-dreamscape definitely lessened the stakes, hence why I think throwing some of the episodes around to conceal what was going on with Dick may have helped the impact a bit.
Also, I'm slightly in love with Donna Troy.