Well, I suppose one of the things in its favour is its excellent female characters and the way they're treated; the male:female split amongst the central cast is almost completely even, which is incredibly rare even in canons that don't have twenty-something significant characters, and the female characters all have distinct personalities, plotlines and motivations of their own. It's sort of sad; it seems like such a small thing - 'give the female characters as much significance as the male ones' - and yet actually finding something that achieves that really brings home how rare it is.

Fandom-wise, the even gender ratio and the huge cast probably brings in 'shippers of all stripes; whether you like slash, het or femslash, Homestuck can provide both subtext and canon, and the wide range of characters allows for a huge range of relationship dynamics. Meanwhile, it's still fundamentally a story of friendship and adventure, so people who aren't particularly 'shippy can still enjoy it. Maybe it's just a 'something for everyone' thing? I'm not sure whether that really explains why it became so astonishingly popular, though, and I don't know how the fandom made such a bad name for itself.