Sevii Islands. You are made to get a Ruby and Sapphire to help Bill upgrade his storage system to link up the trade feature with Hoenn.
Also Bulbapedia has info on Bill's letter to Lanette.
Hoenn
While visiting Lanette in Pokémon Ruby, Sapphire, and Emerald, players can check one of her computers to find an E-mail from Bill. The English translation of the E-mail makes it seem as if Bill is crediting Lanette for upgrading his system, whereas the Japanese text clearly establishes that he and Lanette are co-developers of the original system.
English Letter:
"... ... ... ... ... ... ...
Your storage system
offers more convenience than mine.
It has a lot of user friendly features that
make it fun and useful too. It makes me
proud that I played a part in its development.
Here's hoping that you'll continue
research in Storage Systems.
From Bill
... ... ... ... ... ... ... ..."
@Forever
Well you can look at the severity of Galactic/Rocket over Magma/Aqua.
Galactic/Rocket wanted to Rule the world in some fashion, much like Plasma was trying to do. They both had different ways of doing so...Galactic in an attempt to control God like Legendaries, rocket through sheer force, money, and nastiness.
Magma/Ruby were basically Extreme PETA fighting for better living conditions for Pokemon that they seemed to like. Aqua, Pokemon of the Seas. Magma, Pokemon of the lands. They didn't essentially fail like Rocket and Galactic did. In fact they succeeded in acomplishing their goals for a short period, but then learned the error of their ways as the Legends they fought to control proved too powerful for them. Kyogre was flooding too much while Groudon was evaporating too much water and completely destroying the ecosystems. Both also willingly gave up their ideals in pursuit of peace and a more fair living. So its not that it was seen as a failure...its just that methods didn't match to the current plot method AND that the teams easily gave up when they were succeeding.