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I think mega Latios and Latias have differently-shaped eyes.
Not sure about the shape, but they do have differently coloured eyes - Latios's are red, while Latias's are yellow (same as their base forms).
Edit: Actually now that you mention it, I'm comparing the models (Latios, Latias), and in fact when they Mega Evolve, their eye shapes become more alike. Normally, Latios's eyes are a lot narrower than Latias's. Mega Latias does have slightly larger irises than Mega Latios, though. Physiologically, base Latias and Latios also have some other notable differences that the Megas lack - such as Latios having larger "foot" fins (which protrude straight rather than at an angle) and longer head fins.
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