I think the moveset creation, model creation and animation, balancing issues and the like take up far more time to do than the single player things. I honestly don't think that the time it takes to do 2 stories (if there are expansive individual ones, this is taking into account that we know virtually nothing about the single player aspect of Brawl and each character's inclusion could be a small part in 1 giant story) is equal to the 1 of the previously mentioned aspects. And what of ZSS? She should count as 1 too, and yet by your system she's only what, 2/3? That would pretty much force everyone to include at least 1 clone on their list but then again the 1/3 was by Melee's standards and since each clone would have to have their own individual story (maybe) then they'd be more like 1/2. So instead of getting into 1/2's and 1/3's, could we just stick to clones = 1/3, transformations = 1? ;pAnyway PT is more like 2 character seeing as a few of his stuff (Story etc) will only be for 1 person so the work he saved from that would be put into creating another character.
The way I see it is this:
Transformations: Needs everything that a regular character does, bar certain aspects which include: Single Player (unknown, thus could range from hardly any production time to 1/2 of the production time for all we know), stage (if each character gets their own stage, purely speculation as it didn't happen in Melee so probably should get ignored until proof) and character portrait (negligible I'm sure). This is remembering that Sheik had his/her/it's/potatoe's own sounds/model/animation/moveset/victory pose in Melee.
Additional production time added in since it vastly effects the balancing of a single character. Make the transformation too strong and it either needs to be toned down or some method from stopping it being abused. The PT employs Stamina, which avoids the abuse of 1 Pokemon against an opponent that it may have an advantage over. The whole character also needs to be re-evaluated and balanced accordingly because a strong character that can transform and adapt to other situations is stronger for it, and thus becomes too strong. This means that both the original character and the transformation need to be designed in tandam for balance. In the case of PT, this means a 3 way balance attempting to make a character balanced that is adapatable to many situations but can't be too weak in their own right to make sure that each Pokemon can hold it's own with a skilled player. There's no point being adaptable if each of your characters is more like a different type of Pichu after all (or insert other useless Melee character in here).
So it comes down to an undefined time save of cutting the single player against gross balancing issues. Considering that they're going to strive for perfect balance, after all no characters are designed to be vastly overpowered but they just end up that way and others significantly more useless, this is going to have an affect on the production time. How big an affect? Well that of course is pure speculation, I know I'd have a hard time trying to balance a 3-way character transformation up against a potential cast of 40 other characters.
@PrettyGoodYear
It's not about the roster size, it's about the production time. *proceeds to bash head against wall*