Still speaking off the top of my head here, with no real research done, but it looks to me that we have two important pieces of information, organizationally speaking:
1. Domain (or General collecting category, or Area of interest). This is a loose designation, that can be applied to anything that a collector feels puts a particular item into his area of interest. The most obvious example is "Transformers", with other examples being "G.I.Joe", "Marvel", "Star Wars", "Thundercats", etc. (We might have more broad ones as well, like "action figures", "stamps", or "bobble-heads"). Brand does not matter. For example, Revol-Tech Convoy gets the "Transformers" domain, even though it is technically from the "Revol-Tech" brand.
Logically, any toy or item should be able to support multiple domains. Transformers: Crossovers Luke Skywalker would get "Transformers" and "Star Wars".
2. Brand. Not sure about this, but I believe that toys only ever need one brand. "Transformers: Crossovers", "Transformers: Cybertron", and "Dark of the Moon" are all brands. In our current model, the brand is usually what we think of as "subline", and it's positioned in our category tree between the country node (which will be going away) and the class nodes ("deluxe", "leader", etc).
Maybe what we should do is sort of keep the "brand" in the category tree as it is now, but add this notion of "domain" to the mix, to be used as a filter.
Way back when I started on this (yes, I planned on expanding to other toylines from day one), I envisioned a series of tabs across the top of the site, with labels like "Transformers", "Star Wars", and "G.I.Joe", with the idea being that you click on any of them and sort of flavor your whole site experience towards that domain (you know how we have Transformers parts floating through the shmax logo in the header? How cool would it be if they turned into green guns and whatnot for G.I.Joe?).
Technically, it would be a filter behind the scenes, such that if you filter by "Transformers", only items tagged as such, and their resultant brands/sublines would show in the nav menu.
Am I on the right track, Spaceharfang?