I don't know enough about the economic considerations of the industry, but from a consumer's perspective, I'd say both options are good, and its a pity when we have only one or the other. It would have been cool, for instance, back in Combiner Wars to have had the Constructicons sold separately. They definitely look like good toys in their own right, and in-story are possibly of more value to the Decepticons individually than the members of any other combiner team.

On the other hand, gift sets are nifty. I never had that as a kid, so when I got Victorion (preferencing a character I'd never heard of before) I was stoked by the packaging and sense of completeness that comes with it. For this reason, I keep them in box most of the time, and the packaging is definitely part of the charm.

Overall, I feel that more coherence to what is released in what waves would be good. At any one time we should be able to get toys from different factions, at different prices, and with consistent themes.

Having said that, some thought does seem to go into the planning of Transformers. For instance, over the course of the Prime Wars Triology, each Insecticon was released, one per chapter, so that after a few years you could get all three. It would be even better if we'd been told that in advance.