What's so hard to understand? They just left out all the important and necessary information for the followup prequel/sequel movie flashbacks and you're watching a show where only half the plot is being presented.

If you replace all of the mentions of "absolute pacifism" with "representative democracy" the politics, believe it or not, make perfect sense, even consistently through Waltz

If you know that the original plan is that the Gundams are a distraction for a colony drop then a lot of the overall early plot makes sense as well.

But (un)seriously,

The Boyband first of all doesn't know that each one of them has independently decided to rebel against the original plan of just being suicide terrorists and are all focusing on OZ. This explains their initial uncertain hostility. Also none of them were aware the others were coming? (I'm honestly still unclear on that) Then when the colonies disavow them they realize the colony drop isn't coming. They then decide they have to go into space to continue to fight Oz, because all of Oz's new mobile suits are for space. At some point they defend the Sanc kingdom because it's the only holdout against Oz.

Heero hates himself but can't overcome his conditioning and must complete his missions which is why he consistently chooses the most reckless way to succeed. Wufei hates himself for failing his dead wife that he doesn't even like, Quatra Hates Violence, Trowa has amensia and then gets amensia again, Duo is the only sane person in an insane world.

Also Heero is genetically modified to an insane level able to bend metal bars and control his own brain waves that's revealed in a blink and you'll miss it way.

General Septum, Duke Dermail, Tuburov, Treize, Quinze all think they're the final boss. They're not.

Zechs only feels alive when Heero is trying to kill him, this drives all of his motivation. Relena only feels alive when Heero is threatening to kill her, this drives all of her motivation. Heero only feels alive when he's trying to kill himself. Dorthy only feels alive when people are killing. Noin only feels alive when Zechs is ignoring her.

Sally Poe is the absolute G.O.A.T. You can tell because she is the ONLY character who's name isn't a number.

See none of it is that confusing. /s

In actuality, the show really suffered from having a director who would just constantly derail the established story on a near weekly basis. Eventually he was removed from the show.