I think at this point, there is a clear problem with Toss at the high level play. Only 12 out of 64 qualifying for GSL3? Tester, Inca, Huk, Kiwikaki, and LegalMind all knocked out. It seems that the toss who got through simply didnt have to deal with any decent T or Z players. People say that
"Toss isnt underpowered. Look at the sc2ranks statistics:
http://sc2ranks.com/stats/league/all/1/all. More diamond tosses than anything else."
Here is the thing though. Most players who play starcraft suck at it. When it comes down to differentiating players at mid and low skill levels, balance often times has nothing to do with it. Its all about who is more skilled. The fact that there are so many Protoss at the diamond level simply means that there are more skilled people using protoss(if you want to call diamond skilled). I think there are so many "skilled" Toss players because of the low skill requirement. I am a P player myself, but I consistently play Toss with 5apm lower than Terran, and 10-15 apm lower than zerg. So its easier for people to get "good" with protoss due to fewer mechanics.
So there are more diamond Protoss because its easier to pick up. But what happens to all of these people once they get to diamond?
Ultimately, your skill level takes you as far as you can, but the best place to look for balance issues is the place where people play the game near optimally(at the pro level). In the first GSL, the game was still new so players were not playing the game "optimally" A lot of protoss qualified probably because they picked up protoss well and had not hit the skill cap yet. But these protoss didnt go too far(none into the semis). In the second GSL, fewer toss made it through, and those that did didnt advance as far. (only one in the RO8 i think). As more players are hitting the skill cap with Protoss, and the Terran and Zerg players are still improving due to more difficult mechanics, the balance issues are becoming more obvious. Now at the GSL3, when lots of players have hit the skill cap for protoss, and zerg and terran have further improved, we have less than half the P players compared to T and Z(12 vs 24 and 27). They need to buff protoss at high level play, but only do so through a difficult mechanic(similar to marines for example), and at the same time nerf some of the "easy to use" but potentially devastating options for Protoss like collosos (any noob can get collosus and win. but pros can consistently counter them now)
TL;DR
Protoss has a low skill cap which makes it easier to learn so many people are "good". But at high level when the game is played near optimally, protoss in underpowered. Fix it by making it harder to play but more powerful if you play it well.