It can't really be biased when the results were voted for. After all,
Puella Magi Madoka Magica has been dominating the sales charts, so obviously a lot of people like it.
EDIT:
Madoka Magica Wins 12 of 21 Newtype Anime Awards - News - Anime News Network
AnimeNewsNetwork have elaborated that
Tiger & Bunny won Best Mecha,
Tales of Xillia won Game Opening Animation and that
The IDOLM@STER actually won Best Commercial.
Also, to quote the article:
(Unlike other awards, particularly overseas, the Newtype Anime Awards for acting are not given for specific roles.) . (Although I bet Madoka and Okabe certainly helped xD).
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