Overall coolness
Your series has an overall coolness factor. You use a few NG characters and you put them in a believable setting with ambience and nice lighting.
I particularly enjoyed the Flash file surfing, that was creative and I would liked to have seen more interactivity between the characters as they glided toward the crown.
Mega Knox was cool, even if it were only a cheap 3d model with bad animation.
The inclusion of the Stick Mafia was kinda lame, especially since they aren't even in the Portal yet. Sure, the creator asked you to put him in, and I'm sure that Flash is very nice, but you know, there are a lot of other characters/series that you didn't include (or gave even shorter cameos to) that other reviewers have already mentioned. You shouldn't need to be asked for you to have included more of the Portal's favorites (Foamy, Compasses, Madness, and I Love Egg were nice, albeit brief).
As synj mentioned before, even though you made fun of yourself for the cop-out ending, it still doesn't alleviate the fact that it's a cop-out. The ending was expected, but the king comes in for a second and gets his crown whereas the others have been battling it out for the last 3 installments? That's just cheap.
I hope whatever your next endeavor is, you think about the animation. You've mentioned to some others I know (via email) how you aren't good at animating and just happened to composite all the separate 3D renders together. Although the compositing/rendering is well done, it doesn't make up for the lack of animation (and any animation thereof consisted of a lot of rotation; just think Lengendary Frog and you begin to realize that rotation doesn't equal quality animation).
You surely don't deserve to be the Top Rated Artist on NG. Battle For the Portal is overrated. You have attested to this in personal emails, but you would never mention that here. Bask in your glory that is the one-eyed man in the land of the 3d blind.
(Side note to other reviewers: You can't nominate SecretAgentBob as the King. He's not a character in the Portal, he's the author. e.g. Knox can't be King, but you can nominate Knox's clay army)
You've got a lot of potential to make a real blockbuster, not just one that the kiddies find entertaining because it has a lot of smooth 3d renders in it. You are pretty good at direction (even if it is about cheating in part one, i.e. the flag shots), and your talents in that area would be greatly enhanced if you team up with someone who lacks those skills and are better at animation than you. You might even be able to make another tribute movie that actually includes many of the characters you're paying tribute to!