It doesn't seem to be true that all popes before him were canonized; Pope Boniface II wasn't, for example.

It's hard to prove why something didn't happen--we don't have records of someone suggesting that he be made a saint and other people shooting them down, as far as I know--but everything about Pope Vigilius screamed against canonizing him. He came to office by essentially driving his predecessor (Silverius, who was made a saint) out by force of arms, after gaining the support of Empress Theodora by promising to support heretical doctrine (in particular, the doctrine that Christ was purely divine, rather than human and divine--he went back on his word, possibly for spiritual reasons, possibly because he didn't want to lose the support of the Orthodoxy), and his reign was mostly marked by his humiliating failure at handling the Three Chapters controversy(1), during which Emperor Justinian bullied him into condemning the Three Chapters after he had very publicly refused to do so. John Norwich ("Absolute Monarchs," from which I'm pulling this information) describes him as leaving the "papal prestige in tatters."

(1) Long story, very short: there were two branches of Christianity at odds with one another, the orthodoxy and the monophysites, who followed the above-mentioned heresy. This was a problem for Emperor Justinian, who had both groups as his subjects and therefore had to tip-toe around trying to not offend either of them. He came up with the idea of trying to rally the support of both groups by condemning a third sect, the Nestorians, who both the orthodoxy and the monophysites hated and who were politically weak enough that he could push them around. He did this by condemning three specific sets of writing, the "Three Chapters." It didn't work. The monophysites wanted real concessions, and the orthodoxy viewed it, correctly, as trying to conciliate their enemies. Pope Vigilius, who first refused to condemn the Three Chapters, then was bullied into condemning them, then tried to compromise by condemning parts of the writings but refusing to condemn the authors, a which was rejected, before completely capitulating, didn't exactly endear himself to anyone.