Hm. I was tired and wasn't thinking clearly so my position that I stated in my post wasn't accurate even remotely (I wasn't sure what I was thinking to be honest), so I deleted it. I think when we talk about "Species Clause" we need to look at it from a larger perspective. I think we can use the Battle Tower guidelines as an aid but it shouldn't be the primary influence on Smogon's decision over this.
He's my short little proposal, for judging over all in a somewhat technical way.
I think whether or not something should be allowed under Species Clause, or whether or not the different "forms" are different enough to permit under Species Clause, should be judged by their Typing, Stat Distribution, Ability, and Move Pool.
Typing wise, if the different forms typing are different they should be for all purposes considered different Pokemon. Typing is such a major part of a Pokemon, determining STAB boosts, weaknesses, etc. that if something has different typing that distinguishes it significantly enough to allow under Species Clause. So, the question that would arise with respect to this are Wormadam's forms and Shaymin's forms different enough with respect to their typing?
For stat distribution, do the stats completely modify the use of the Pokemon? I'd say, in general, this is true. Deoxys-A plays entirely different then Deoxys-D. For all practical purposes they are entirely different Pokemon. Giratina is a bit more iffy on this grounds, but then again, it's had such little play testing it's hard to determine.
Ability: If the abilities change, the Pokemon changes, but is the change enough? For example, if Skarmory uses Sturdy instead of Keen Eye it's still Skarmory. However, if Shaymin get's Serene Grace as opposed to Natural Cure, the Pokeon is played entirely different now.
Movepool wise, do the move pools make them so significantly different that they play in different ways? The Rotom's fall under this category, however, it is a one move difference that seperate them. Is that different enough?
I'd say that Rotom and Giratina are the only questionable thing right now. The others in question should probably be allowed on teams since they play so differently they are , for all practical purposes, entirely different Pokemon. It probably requires more play testing to distinguish the cases of Giratina and Rotom to make a proper conclusion though.