I don't think they should alter the game plan, and they should steer clear of the joker for as long as possible. Like season 3 or 4 (which means first off they make it that far, which hopefully they do).
As for Riddler, I hoped that gets drawn out some more. This season was about the Penguin's rise to the top of Gotham's underworld, while just laying the groundwork for Nygma's turn.That was what I had hoped was the cliffhanger ending to season 1, Oswald takes control of both crime families and Nygma starts sending riddles to the police (and maybe gives that iconic Frank Gorshin like laugh).
Alas, the American public is greedy and has no patience, so they demand things like this and ruin it for everyone. So everyone calm down, and enjoy the ride instead of trying to jump to the destination.