The SNES transparency color counts are a meaningless. It's almost always not used to...
The OP asked his question in a way that could be interpreted as a "hardware superiority" question, or as a "game superiority" question, quite cleverly. However, I do not think it is a good idea to switch the topic from the former to the latter whenever superiority of the SNES, Genesis, etc. on a specific point becomes apparent.
For example: "The TGX wins in # of onscreen colours" "No, the SNES does, technically." "Yeah, but the way they are used..." leads a simple discussion down confusing avenues. # of colours is a measurable hardware stat, while artistic talent is a whole subjective topic to itself.
Comparative capabilities of systems is a very interesting topic in and of itself. Discussions of actual execution are great too, but not in the same breath, because it always causes the logical thread of these discussions to unravel.
Okay, PCE has twice as many tile and sprite palettes as the SNES.
Why even bring transparency up if "number of colors on-screen" was already into execution territory?
The OP actually based this thread purely on an execution based comment though. I've read countless times the details of how and why the PCE is the fastest at animation, but I can never remember the specific details because I'm not a programmer intimately familiar with the inner working of all three consoles.