Overall, season 3 is definitely the weakest one so far:
From the filler episodes in April's farmhouse that went on way too long, to the very rushed finale (Splinter dying and Earth disappearing "is awesome"???), it really wasn't as well-thought-out as the first two seasons. It didn't seem like there were any major developments between the main characters, and is it just me or was there not even a single Raph-centric episode at all?
Still hoping that they can improve on the next season. Get back to creating those moments that we love about the characters. Remember when the turtles were forced to switch weapons? Or when Donnie & Mikey had a feud w/ Leo & Raph? And how about actually developing the whole Donnie-April-Casey situation? Perhaps reignite the Leo vs Raph rivalry to new heights? Also, they need to put a stop to the Mikey-screws-up episodes. It's gotten really tired at this point.