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I think it was supposed to be a play on the fact that Mega Evolutions lose the gender differences of their base forms. For example, male and female Mega Venusaur look the same even though female base Venusaur carry a seed and males don't. Since Latios and Latias are VERY strongly implied to be males and females of the same species (for reference, Gen III is before proper gender differences were introduced as a mechanic, so this was basically the same deal as Nidoran), the Megas converge
I honestly think it's a justified and fairly interesting gimmick in concept, and although it's mildly disappointing in the sense that it was functionally just a way to give us one design instead of two, I do personally find the color scheme on Mega Latios appealing (the purple and white go nicely with its red eyes) so I don't think I would ask for it to be done differently.
Then again, I think I'm one of about five people in existence who actually likes the design they happen to share. While my own take is "one good design is better than two mediocre to bad ones, and it at least makes some sense that they share it," I'm sure plenty of people out there are just wishing at least one of the two had a design they liked, and they were robbed of that chance by both having the same design. I will concede that forcing it on fans of *both* has every reason to be twice as controversial if you don't already like the design.
