(On the other hand, neuroscience and explicitly biological neural modeling are exciting areas, reasonably well-represented at NIPS. Those topics, however, are almost entirely different from neural networks of the multilayer perceptron / [Hyper]NEAT varieties.)
But your criticism of the article seems accurate. ACO isn't new, and there's little evidence that it will solve any of the major outstanding problems in AI.
Less generously, however, I'd suggest that much of the research related to the family of population-based stochastic search methods, ACO, PSO, and HyperNEAT included, is prone to the same risk: the lack of a field-wide theoretical foundation, coupled with the absence of a field-wide standard methodology and benchmark set for empirical comparison (as opposed to, say, the situation in supervised learning), makes it temptingly easy for a particular researcher to believe too strongly in the capabilities of that researcher's pet algorithm. This situation seems to have balkanized the field (page through a recent GECCO proceedings, for example), and holds back wider progress.
That's not to say that HyperNEAT can't do great things. It's a fun approach, and Stanley et al are running far with it. But your boosterism of it, and the boosterism of ACO that you're objecting to, seem closely related.
(For contrast, I'd suggest, eg, the natural gradient work at IDSIA. It's unlikely to be the ultimate method, but may be a good model for solid research in this area.)