I think the problem is that you guys seem to be wanting to look at everything as a black/white, good/evil situation and the situations presented in the TP books are much more complex than that. If that's the only way you're able to look at things, then maybe you should go back to watching Superfriends and leave Trek books to those of us who can see beyond those kinds of simple concepts.
Well, generally if people are calling them the "Legion of Doom" they're saying they're an alliance of evil supervillains. I don't think anyone is denying that they're antagonists, we're just trying to explain that the situation isn't as bad as you guys are trying to make it out to be.
Exactly.
Star Trek has not historically been about pure, one-dimensional evils any more than it's historically been about war. The Romulan commanders we met in "Balance of Terror" and "The Enterprise Incident" were nuanced, sympathetic figures, and BoT made it clear that not all Romulans wanted war. The Klingons in TOS were generally presented as more overtly villainous, but "Errand of Mercy" showed that Kirk and Kor were essentially two of a kind, and included the Organians' prediction that the Klingons would one day become our allies (as they eventually did), and "Day of the Dove" let us see the Klingons in a more sympathetic light and planted the seeds for future reconciliation.
"Enemy" powers in Trek have routinely been explored and given nuance, and have frequently been shown to have factions that disagreed with the hostile policies of their governments. TNG showed us Romulan dissidents and unificationists, DS9 gave us Cardassian dissidents and made both the Romulans and Cardassians our eventual allies, etc. War has usually been a looming threat that was averted through the protagonists' intelligence, cunning, or kindness, or by convincing more moderate voices on the enemy side to prevail. That is
Star Trek's normal way of doing business. The Borg and Dominion were the big exceptions to that rule, but they're both gone now. The Typhon Pact is not meant to be like those exceptions; it's meant to be like the antagonists we've had in the past, the ones that weren't all bad, that had multiple factions and beliefs within their societies, that could usually be persuaded to stand down from war by one means or another. The ones that audiences were invited to feel curiosity and sympathy toward rather than mindless hate and fear.
Of course, that doesn't mean they're not dangerous. There wouldn't be much of a story if they weren't. It just means that the
Star Trek way of addressing a threat is to try to understand it and find common ground, rather than just shooting at it a lot.
Between their plentiful organs and masterful disguises, they could take the Pact to (appropriately enough given their social structure) new heights. 
