Generally, I think people don't like how "Throw-away" some of the legendaries have become, and I'm inclined to agree. Latios and Latias are basically the same thing, in design, but initially, they were version exclusive. Essentially, they're the point GameFreak decided to make one-time monsters version exclusive, which is just an annoying way to cheaply differentiate the versions in order to warrant buying the same game twice.
Beyond that, do you remember the legendary trio in DPPt? Uxie, Mesprit, and that third one of whom I can't even recall the name. The three of them had, again, the same basic design, and yes, while they did fight differently, having one Pokemon instead of three, or even having that one evolve to represent each one, would have been a lot less... redundant. The stat/move pools of the other two could have been used in something like a Spoink evolution or an all-new, original Pokemon.
It's kind of the same reason why people want different starter types than normal: We've got Pokemon that represent the old types, and there's so many new types, so I think most fans want to see progress. The idea behind the DPPt trio actually fits into this, for once, their typing isn't a one-way triangle, instead, they each develop secondary typing such that the "SUPER-EFFECTIVE" arrows go both ways.
Also, people don't understand what the point is of something like Phione. Why have Manaphy have a weaker offspring lacking some signature attacks, if said offspring can never evolve into Manaphy? There's literally no reason, it's just excessive. If Manaphy could bear something unique and self-sustaining in an egg, that would be one thing, but Phione is just an inferior Manaphy.
So really, I'd say most fans just want legendaries that fit into the game without being redundant of each other. While some might argue that the bird and gerbil trio match this description, there were fewer general legendaries, initially, and in truth, their designs were much, much different from each other in comparison to what you currently see in the RSE and DPPt trios.