Well, here's the thing. All the stuff you just described? They were triumphs of the people running Clark and Greeley and their fellow travelers.
Those guys? Were not jokes. They fomented a war that was only marginally less bad than the War of Corporate Occupation and left the whole of Known Space politically destabilized and bereft of a strong body of interstellar diplomacy, peacekeeping, and lawmaking. It didn't quite go as well as they'd have liked (they didn't manage to break the back of Earth as the cultural hub of the human diaspora) but it went really well. You're right about that. We don't even know who they are, really; the Mysterons are probably yet another front.
But the Earth Alliance itself? They're kind of a joke, and comically inept. All the things they did were things that were going to culminate in them getting their asses kicked. The fact that they worked temporarily doesn't really change that.
It's like... mmm. Imagine a guy who sticks up a 7-11 and, instead of just bailing with the register contents immediately, sticks around getting drunk off malt liquor and ordering the cashier and customers to dance for his amusement. Now, what are you going to think? "That guy has things going all his own way; he got a bunch of money and booze and all these people are terrified of him and doing what he wants?"
Or are you going to think "This idiot is going to die in a hail of gunfire the second the cops roll up and he staggers out the front door waving his .22 around."
The EA is that drunk stick-up artist, in my mind. Everything they did was so obviously, painfully designed, not to build them up into a long-lasting, stable, Evil Empire, but to inflame the situation around them until they imploded under the weight of their own incompetence and arrogance.
Sidebar: I'm not sure about some of the more Federation-wide stuff you list them having gotten away with. The scope of Federation power and authority has, I think, changed somewhat since Day of Infamy came out. I think to the current production team, it is a much weaker polity overall than it once was.