SC2 isn't as popular as Brood War because of balance issues that won't be fully worked out until (at least) 6 months after the last expansion.
I don't know, SC2 may be more balanced than BW at this point. ZvT is bad because of fungal growth but it's no BW ZvP.
SC2 likely isn't as popular as it could be because it's just kind of boring. Blizzard replaced inventive, exciting units like Defilers and Vultures with bland one-dimensional ones, and did a lot to homogenize the 3 races with units like Roaches and Marauders. Unfortunately it doesn't look like a whole lot will change with HOTS either.