This thread is six years old but where else are you gonna throw out random ideas, huh?
I was playing through Shattered Dimensions recently, and (spoilers for that) there's a part where an NPC speculates that the heavy snowfall is caused by a Pokemon. When I saw the alternate dimension was sunny, I thought that it was going to turn out that in one dimension, there was a stand-alone legendary like Heatran causing the snowy weather, and in the other, a different legendary that fit the same role in the story but with a totally different legend and powers. I got to thinking about what that might look like with some of our canon legendaries!
- Mew/Mewtwo - Switch their roles with Arceus and the Type: Null line! Gladion escapes the Aether Paradise with a grumpy cat in a clunky helmet, who evolves and can learn every move through the M.E.W.v2 System, while in Cerulean Cave, a horned creature with the ability to change types hones its powers... (And if you believe in the "Ditto is a failed clone of Mew" theory, maybe Cinnabar Mansion has curious little deer scampering about with Color Change as their ability)
- Legendary beasts - Three Pokemon were killed during the creation of the Brass Tower - a Grass-type, as wood was cut to build it, a Ground-type, as the foundation was being set, and a Steel-type, as the brass was being melded. It's said their spirits still haunt the tower's floors, though the tower's guardian manages to keep them confined within...
- Regis - Five artistic Pokemon collaborated together on a masterwork, a mosaic-like golem with traces of each creator within.
- Lunar Duo - A lunar trio, with a gibbous, a half moon, and a full moon Pokemon! (not sure what they'd represent - non-REM sleep, maybe...?)
- Lake Trio - Three Steel-types based on Asimov's laws of robotics - one for obedience, one for self-protection, one for protecting humans.
- Swords of Justice - A Dark-type group based on some famous villain team instead!
(I guess this isn't really "fitting the same role in the story with different powers" so much as "having a different story entirely", haha)