The protoforms were the ones stolen by Lockdown from Prowl's master (in five servos of doom), and sold to Starscream. Starscream then used some to make his clones, but somehow one landed on Earth and Sumdac found it, accidently activating it to turn into Sari. The remaining protoforms appeared to be destroyed by Megatron in the previous episode, to prevent Starscream from getting a new body, but Sari managed to find one (and looked to be activating it). That appears to be a loose end though. It did look like the final scene in the final episode that they still had 3 protoforms, or maybe they were just closed caskets of fallen Decepticons?

I felt it wrapped up a bit too quickly, with a number of loose ends - specifically all the other characters that are still running around on Earth. And Magnus should have made an appearance at the end to show that he was still alive.
And who else thought it was a big tease for the Lugnut Drones to land on Dinobot Island, and then not have the Dinobots appear?

I was surprised that Starscream's spark crystal was ripped out of his head, but none of the other Earth-made TFs were (or maybe they did, and they are all now dead too).