For one the dialogue in GenIV actually made me feel like it thought I was fucking retarded. Never in any of the generations has the character dialogue been that bad. Secondly, the motives for why the evil super-generic Team Galactic, who resemble a bunch of Lady Gaga background dancers, are trying to summon [GOD-BEAST] is never really explained. Why was Cyrus trying to summon the legendary? To rule the world, I guess? That's usually it. How did he intend to control it? The orb things? I don't recall it ever mentioning those controlled them, only that they summoned them.
Every other evil organization had some plan.
Rockets took over Silph Co, the largest company in the Pokemon universe to expand their organization because they wished to dominate the world using Pokemon in general. They created Mewtwo, but he questioned why he should follow orders from lowly humans and escaped.
Teams Aqua and Magma wanted to change the face of the Earth for their (admittedly sort of dumb in Aqua's stance) plans to expand life, and planned to use one of two orbs to control their specific legend. It backfired, however, and the beasts raged out of control, to which they saw the error of their ways.
Plasma was basically protrayed as PETA, but in truth it was all a guise set up by their leader to dominate the world, destroying the mind of a young boy in the process to control the power of the version legendary.
Also, the designs for the Pokemon in GenIV all mostly sucked.
It's all in the dialogue.