I happen to strongly disagree with Yahtzee's statement that the whipfist is the only power anyone would want to use. It's good against soldiers, and it's great to hijack helicopters, but against Hunters, supersoldiers and any sort of armor you really want the blade: the jump-charge-and-slice-down attack is stupidly damaging.
The other two attack powers (big fists and claws) aren't as useful: the fists, I'll be honest, I didn't unlock until restarting the game in plus mode, and even then I found myself only using them for novelty, and the claws don't deal very much damage by themselves. Sure, you have the underground spike attack, but its range is too short, it's way too slow and once the attack is done there's a delay of two or so seconds until Alex can move again, so I found it a great way to lose a lot of health very quickly.
Yahtzee also seems to have missed an important point of Prototype: the game is not about being as efficient as possible in combat. If you play it like that then yeah, you won't be upgrading many things, because the whipfist and blade will dispose of everything the game throws at you. Prototype's combat is mainly about the rule of cool [http://tvtropes.org/pmwiki/pmwiki.php/Main/RuleOfCool]. When you can shoryuken a marine (or Hunter...) in the air, punch him thrice in midair then slam him into the ground like a rail spike, and then feel all stylish and cool for pulling it off, THAT's what Prototype is about.
Also helicopters + whipfist = stupid amounts of fun. I've had loads of fun flying around in gunships doing random damage to bases and hives, and swapping helicopters as they get damaged by ejecting from one and whipfisting right onto another one. It's fun to see how long you can keep this up without touching the ground. I think my best was eight gunships before missing a whipfist grapple attack and falling.