The same plot gets used over and over again, one Titan going rogue, challenging the bad guy alone even if its obvious that it is a trap and, predictably, loses.
And the constant Deus Ex Machina in the form of raising the dead, not only through the Pit but also now just because they walk over a bridge in the afterlife. Yes, in the comics the dead rarely stay dead, but raising so many characters in such a short time gets boring.
And then there are all the plot holes. Why does Waynetech build heart monitor bombs? Thats something I would expect from Luthor. What is even the market for that? How did they get more than one even though the one used on Hank was supposed to be the only prototype? The others didn't look home made. Where did Crane get all the money to bribe so much of the GCPD to take full control over the city? We are talking about hundreds of people and considering what they were willing to do that could not have been cheap. And if it was, why didn't the mobsters already do this?
Why was Gotham quarantined and how did the population get water during the quarantine when the normal water supply was shut off?
And of course the already mentioned Superman problem of why didn't Conner solve everything instantly as soon as they knew where Crane was? Even the entire last episode was redundant when instead Superboy could just have run in and punched everyone in the face.