I recently heard Dan Kaminsky mention in his recent article:
http://www.wired.com/opinion/2013/05/lets-cut-through-the-bitcoin-hype/ that a mining algorithm friendly to general purpose hardware is superior because it is more inclusive to "the masses", as it wouldn't require specialized hardware to participate, and thus mining would be that much more decentralized.
I haven't read the article yet, but I agree with that proposition.
I doubt this is much of an advantage though, as most people would have to buy high end general purpose hardware specifically to mine anyway in order to remain competitive and profitable, and the barrier to entry for running specialized hardware (ASICs) will soon be just as low.
In a system such as bitcoin's where everyone fights over a piece of the same pie, this is accurate. However, if mining doesn't secure the network, and coins are generally only created when it is profitable to do so, and you provide a system where only a small profit is made from mining, you have the basis for a currency that is ASIC-resistant because the profitability angle simply isn't there--regardless of the hashing algorithm.
Furthermore, having a mining algorithm require specialized hardware appears to be a great strength. E.g. suppose an attacker amasses >50% of total hashing power. Then the network could (as a last resort) swap out the mining algorithm, and render all of his equipment useless for attacking the new system and for resale. With general purpose equipment, he could keep attacking the new mining algorithm, or resell his equipment to recoup some of his costs.
If you separate network security from mining, this isn't an issue. General purpose hardware can either profitably or unprofitably create money without threatening network security. If the intent is to cause inflation, the attacker is burning value at a consistent loss. If it is unprofitable and there aren't any irrational actors in play, no new money is created.
While the honest miners would lose all of their investment (this should be considered an inherent risk of being in the mining business), they still collectively lose less than the attacker.
You are willing to cause billions of losses in the form of having to buy new specialized hardware for honest people to not only create the rest of the money supply, but also to secure the network. This is terribly inefficient, and it means the attacker has probably achieved his objective of crashing the network. This isn't a "win" by any means. Instead voting to switch the algorithm to something that is again friendly to general purpose hardware is the solution if an attacker has spent millions creating a specialized one.
For some ideas on how to really fix these problems, I have proposed Decrits. The link is in my signature.