1. Zerglings are too big, and in the lesser extent so are Ultralisks. (Design and Pathing Issues)
This problem is widely recognized among Zerg users, Zerglings are just too big. They have trouble producing dps against buildings because of it. This means each Zergling needs more surface area to deal damage. It works "okay" against units, but against buildings you just lack that damage output. Especially against clustered buildings such as Terran "wall-ins". Also the pathing is problematic as well, when you're attacking in a confined space all of your zerglings will try to enter the same pathway, causing them to become clustered and just "dance" around. Once again leading to less damage output. You have to manually make a group follow a different path to reach it's target. Even then this sometimes doesn't work out too well. Ultralisks essentially suffer from the same problems. They just act like giant zerglings, and spend most of their time bumbling over each other. Zerglings should also be capable of passing underneath ultralisk, just like units can walk under a colossus. This would raise the damage output from both units, as well keep very true to the "swarm" feel Zerg is supposed to have.
2. Roaches are dead end tech, and are easily countered.
Roaches are a very niche unit, I was under the impression that Blizzard was going to make every unit have their uses throughout the game. However roaches are not very good once the game reaches a certain level. Their upgrades are also all T2 which requires more time to make the unit useful. Their biggest problem though lays in the fact that their useless against air. Which is problematic to say the least, for a few reasons. Zerg has no defense against early air. Zerglings, Banelings, and Roaches cannot attack air. When we look at the other races they have Marines, Stalkers, and Sentries. Sentries are not so great against air but the point still stands. Zerg is essentially left with queens which do not make good air defense. Meanwhile the other races have excellent early AA units. This makes roaches a bad investment unless you can win by keeping on early pressure with them. They're also countered very well by stalkers, marauders, and especially tanks. They're just not good units. I feel they need a revamp of some sort to make them more useful and more enticing.
3. The current ladder maps are bad.
A lot of the Blizzard maps are gimmicky and they have very bad natural expansion spots. Majority of them are wide open and very hard for a Zerg to defend early game. Also Blizzard felt the need to add destructible rocks, and cliffs everywhere; to flaunt their new unit abilities, and game mechanics. However Zerg doesn't benefit from any of these. Not only does zerg lack high dps early game to take advantage of destructible rocks, but they have almost no way to combat cliff drops. This was problematic in Broodwar I can admit, but it's so much worse in Sc2 since you can no longer shoot up a cliff unless you have vision from an aerial unit. Zerg has a very tough time dealing with reaper harass early game, and every map is conveniently loaded with cliffs all over. It's very difficult to defend, and you're always vulnerable to harassment.
4. Zerg isn't very intuitive or versatile.
When compared to Terran, and even Protoss. Zerg isn't left with very many options. Your whole game seems to based around struggling to survive and reacting to everything your opponent does by making hardcounters. This may not be a problem but Zerg has a difficult time scouting until Early/Mid T2. This leaves you very vulnerable to attack. You might make mutalisks only to find your opponent has made vikings or phoenix. You might make hydralisks to find your opponent has made tanks, or colossi. The list goes on and on. It seems the only units that are solid in the zerg arsenal is a lot of zerglings and infestors. This makes them a boring and difficult race to use. Broodwar didn't really share these problems since unit compositions were not very diverse, and the meta game was set. You almost always knew what your opponent was going. It's no surprise that not many people use Zerg compared to the other races.
These are just a few reasons which I feel that Zerg is a bad race. I hope that Blizzard will address these issues down the road, and by that I mean sometime soon.
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