The Dr. Freeze storyline and the performances of BD Wong as Hugo Strange, as well as Alfred, young Bruce especially, Nygma and Penguin were amazing.
I thought Flash S01 was pretty good. Season 2 was shit in comparison. I absolutely hated Jay and it was just too much bs drama. Arrow I stuck with but it made me vomit more and more. Agents of Shield was just some filler in between the DC stuff. LOT is god awful and I thought it was the worst of all the shows but somehow the season finale redeemed it somewhat and I am amazed that it was better then the pile of dung that was Arrow.
All of those shows though pale in comparison to Gotham. I made some post a while back where I said it was like Tim Burton's Batman, the Animated Series and Dark Knight had a threesome and it was wonderful.
Everything in season 2 was great in Gotham. It is the only show imho out of all of these that will stand the test of time. The CGI is used sparingly and is done well (just look at Freeze). It's devoid of bs CW teen/Olicity emotional drama, it has great sets, shit actually make sense as far as storytelling, there aren't many plot holes (if any), everything got tied up nicely in the finalle, and the characters and their behavior actually makes sense (and they have chemistry amongst each other).
Shit just makes sense over there and there are so many little nuances and tells to fans (like Azrael standing on the bridge with his cape channeling Batman and Bruce's reaction upon seeing him during the police shootout for example or joker's laugh at the end).
I agree with you OP that instead of doing the same villain or scary monster of the week they made a great season long story and it paid off. They had time to develop every single character and make them real and compelling. I absolutely loved Hugo Strange and Ms. Peabody. penguins story, and Nygma's were also compelling. Everyone even the minor villains got enough screentime for their origin stories to be believable and their actions and motivations realistic unlike some of the random shit that happened on Flash or Arrow.
I really enjoyed season 2 of Gotham and the finalle was pretty good (except for the bomb defuse scene) and made you really want to see what happens next.