Well, the 3rd World War in Trek did a lot to change things. Mainly, the idea (postulated by Trek/B5 fans who do these fusion universes) is that the war pretty much wiped out the MegaCorportations and most of the more corrupt elements of Human Governments. That the survivors were brought out of the dark times by benevolent aliens did a lot to nip xenophobia and pro-human forces in the bud.
There are still Anti-Alien groups like Terra Prime around. So the MegaCorps and Xenophobes would have less power in the fused universe.