The main problems are the voice acting, and pacing/plot.
The voices sound like young kids on bad mics, sorry, but it's the truth. I'm certainly not saying that the actor for the Doctor has to sound exactly like one of the TV incarnations, but he has to sound like he could be one of them.
The dialogue was un-interesting, and combining that with the voice acting caused the whole thing to become fairly boring. Some more movement on the speakers parts would help, since most of it was nothing but still pictures with the mouth animation. But you may want to try to make the story itself more interesting and fulfilling.
There wasn't much of a sense of urgency, and it felt like it went from talking scene, to talking scene, with very little in between. The climax was...meh. While the turret scenes were fine, all the excitement went out when the Doctor had his conversation with the alien. Then, the camera switches right back to the action, the humans blow up the planes, and then Wham! they're saying their goodbyes. That caused the only "Climax-like" scenes to be split up by another talking sequence, and therefore their effect was, for the most part, nullified.
You animation quality isn't bad at all, so next time, I'd recommend skipping the mouth animation, and spending that time on more animated scenes, and polishing the script. Really, just try add more interesting parts. I understand if you don't want to change voice actors halfway through a series, but you'll really have to step up everything else to make up for it. Especially the script.
Concentrate on quality, not quantity. Your viewers will be thankful if you do. 