Not sure if it counts as a mystery or conspiracy, but I've been thinking this morning... and a question pops up: Is it possible that Latios and Latias (Moreso the former) have some kind of reference to Superman?
They are birds, they are planes, they are blue and red, they have a symbol on their chests/torsos...
Hmm, and they do have a triangle on their chest...
BUT I'm going with coincidence. The origins of the Eon Duo is complicated. It looks like they first started off as
a concept image. Whatever the original intent of this Pokemon was, either be the final evo of the Fire-type starter or a Legendary creature (or completely something else), we can see possibly what more of its origin was based on: a jet plane/bird hybrid. However somewhere in development it was decided to split it into two Pokemon, the design was re-molded into what we know as Blaziken but the body shape was made into Latias. This is probably where, now shed of its bird origin, it gained a dragon. However the designers might have thought it was lacking somewhere, either thinking the design was too simplistic for a Legendary or the lore behind it wasn't strong, so decided to give it a blue verion, Latios. There could be many reasoning for that: they wanted to them to have Yin and Yang imagery, they based them on the Aeons of Gnoticisim, etc..
My point is, we know their origin point and from that I think we can form a loose trail of dots how they came to be what they are and no where do I see a Superman influence.
Though all of this does make me want to hear how each Pokemon (or at least the rejected ones) was developed. How they came up with the concept, the reasoning behind the design, how many designs and approvals does a Pokemon need to go through before getting to its final stage. It would make for a neat book idea, give the customers an inside look of what goes behind the GF doors (plus make use of all those prototype drawings they have (though then again they might use some for ideas for another Pokemon so who knows if they would want to release them)).