Its not the twists that are confusing but the actual conflict in general. You start out with something really basic albeit involving the worst plan of all time: give children invincible robots and not tell them about each other even though they are expected to cooperate. Then you have these pacifist dudes that are all about peace but are constantly getting bailed out in obviously non-pacifistic ways. Then white fang shows up and dudes can't decide what their names are.
The twists in the series are confusing to follow because you have a lot of love interests (five separate couplings for the main protagonists) and a cast of characters who are constantly defecting to both sides of the conflict, when not claiming to be independent. And then you have Zechs who is even harder to follow due to his identity and motives switching up all the time.
This seems to me like a misunderstanding by the writers on what impenetrable armor would be like. Almost like it has hit points or something. Regardless it doesn't really matter, for all intents and purposes the fights lack dramatic tension because not only do you not have to worry about the protagonists dying -- at any given the time the stakes could be something you only just learned about.
The gundams weren't invincible, just nigh invulnerable. They could be hurt with a lot of firepower, against a lot of skilled opposition and few lucky shots. I mean, they are being constantly repaired throughout the series.