I don't think that Moore intended anyone to side with Ozymandias at the end of the book, you, me and anyone who reads it all side with Rorschach at the end. I think you weren't supposed to actually buy the alien completely, to show:
How Rorschach, despite being a right wing nut is the one character anyone sympathises with;
That Nite Owl and Silk Spectre are pretty weak for accepting to hide Ozymandias' exaggerated story;
Ozymandias' emphatic "I DID IT" says to me that despite all his "oh lol i had to do something real bad to save lots of people lolol" crap Ozymandias really did the whole thing for himself.
And that Jon truly doesn't care about humans. (And if you talk about the characters following conventions, how would Jon fit into that? EVERY superman style character ever has an overstated empathy for the characters around them. I think it's much more realistic that a genuine superhuman being would act like superman.)
Also i dont think your Limp Bizkit analogy holds up

The book does use comic conventions, but i think it (more to its credit) flips them. Sure, some are predictable maybe, but some aren't and the more predictable ones (ie the fact that no one is really "good") are at least realistic.
IE - almost all the characters have an origin story, yet most (Silk Spectre, Nite Owl, Rorschach, Ozymandias) present the heroes origins being in human terms (child abuse, mum pushed her into it etc).
Im kind of all over the place, but i also will admit the ending was weaker than the rest (specifically because I dont like Ozymandias), but i still stand by hating Ozymandias at the end as being exactly what Moore planned.
Plus the way the story interconnects between characters, times, artwork, to compare/foreshadow is excellent, especially the Black Freighter story. And I'm a huge fan of the art as well, I love how restrained(?) it is.
Out of curiosity, have you read Moore's Supreme: Story of the year Zad?