Maybe Janus secretly likes Tina. Who knows?
Speaking of Magus, think we ought to have a thread dedicated to how cool he is? That'd be neat. Here's laughing at the guy who commented on how many newbies come straight to this topic. Lots of people join boards just for this one character. (excellent observation, by the way)
And in answer to the topic's title, hell yeah! He is the only boss-turned-PC I know of that you can hate so passionately one chapter, and love so much the next. What makes him cool and appealing is not what makes you like him or hate him, a villain or hero, but the fact that you can argue the point and both sides are strong and valid.
Aesthetically he might be a bit cliche, but it is still executed well. Square took what we all know as the classic, demonic villain, and twisted it into something that defied our expectations of the stereotype. Why would this flat, grim reaper wannabe want to join the good guys? Oh, you mean he's not out to destroy the world and suck out our souls? And he's helping us get our leader back? Now that's cool.
Then, of course, there's his theme song. Some of the best remixes I've heard have come off of this theme song.
And if you need any more evidence, just go check out SooperKreep's depiction of him over in the Submissions section