That's true. But, Blaziken's roll in the anime recently, and please correct me if I'm wrong, was not a major recurring roll, and he was just another Pokémon. Pichu Bros., on the other hand, were given names and were central characters in a short. They are still remembered today, some 5-6, maybe more, years after their debut, and they've rarely made appearances outside of small cameos since then. Blaziken's roll may have been more recent, but the Pichu Bros. are fondly remembered. And, also remember that the PMDT needs to be considered. Pichu Bros. can be made with a rather simple model, since they don't require near as many colors or texturing, seeing as how Blaziken's fur/feathers would probably be made pronounced, similar to Lucario's fur. Also, Pichu Bros'. moveset would require substantially less work, since almost all of Pikachu's code could be ripped, and then modified for attributes such as knockback angle, damage, elemental side-effect, self-damage, etc. Blaziken's moveset would be able to recycle elements from Lucario/Captain Falcon, several elements would have to be revamped, and certain moves completely changed. Finally, Pichu has an entire set of voice clips ready to roll, whereas Blaziken's voice clips would need to be made from scratch.
I sincerely apologize for the wall of text. But, anyway, I see where you're coming from about my idea being contradictory. You know, the whole "Why have a duo if they can be separated so easily" deal. I totally understand. One way, I suppose, that could be solved would be having a concept similar to Ice Climbers in that when they use Agility, they zoom together if they're too far apart (with limited range, of course) and hold hands or something while they use Agility. When one P-Bro. is alone or if they are forcibly separated, it functions just like normal Agility. This makes their survivability as a team much longer, presumably solving that issue, while also allowing the two to keep their distance from the IC's and Pikachu. About the double power thing, I think it could be cranked down a little, to prevent overpowered-ness, while also allowing them to keep the self-damage system. While we're on that, you were correct in the assumption that I imagined it working like Melee's. It could, however, be changed or tweaked for balancing reasons. I would object to it being removed completely because I feel it is one of the things that makes the Pichu Bros. the Pichu Bros. I'm not sure how to fix the steep learning curve, but would guess that my previous two suggestions would at least alleviate it a tiny bit. And, I know you said that balancing the self-damage system would be more work than what it's worth, and I honestly don't know how to respond that with a valid argument. I reckon we would just have to see how the P-Bros.' competitive scene would play out. It may be far easier than predicted, or unfathomably hard. The whole high-learning curve I think you are right about. It's steep, and I think my idea for Agility may fix it up a little bit. Maybe you could suggest something? I would really like to hear your idea on how to fix the learning curve.
Also, I don't think the whole swapping movesets depending on the presence of one Pichu is technically feasible, and I'm pretty sure Wobbling was removed for the IC's P:M debut. Please tell me if I'm wrong about either.