I feel bad for the all the Daggers your legends cut up in the first episode. They serve no other purpose than to give the heroes a common, faceless enemy.
Without them, Setsuna might've well attacked Amuro and Kou!
“But Captain, it’s preposterous!” said Arthur almost hysterically, “It sounds like bad science-fiction!”
No, just mediocre fan-fiction!
No offense, Arbiter
I honestly have no idea what is going, and when I barely got to the point when I accepted that OK, Setsuna, Amuro, Kou and Tiffa team up with the Minerva, you threw other guys into the mix. My suggestion: make the 1st episode about these first guys, let them explore a bit. Then, in the second episode deal with whoever else you want to involve, but a) be precise about who's where and b) don't mix too many characters together as it becomes very hard to follow the events, dialogue, and motivations of each character. For example, seeing Amuro and Setsuna alone having it out (verbally) would be more than enough for one episode.
Episode two had more typos:
You’re tough, I’ll give that but you are surrounded. --> You’re tough, I’ll give you that, but you're surrounded.
Char Aznable had been dead or missing for nearly three years know. --> now
“As I was saying to Captain Ramius here,” said Scirocco, “obviously wanting to steer the conversation back on course, “We need to do two things. ---> Scirocco, obviously
“Is this Banagher your boyfriend?” asked Captain Ramius with a knowing smile.
“No! No, he’s just a very close friend and if he is out there, I’d like to know that he’s okay.”
I'm almost hoping Ramius would tease her more.
When you write dialogue, this is confusing:
“They call me that, but I think of myself as just Tiffa.” Amuro smiled at her.
This is less confusing:
“They call me that, but I think of myself as just Tiffa,” she said, and Amuro smiled at her.
Make sure it's clear who is talking and try to link speech and reaction/expressions together so you don't have to "stop" at every full stop. It makes the text flow better.
I'm still a bit unsure where you're going with the story; while it's intriguing to have such diverse characters interact, the story itself hasn't developed much of a plot. I mean, you could've taken just the Minerva's lot and made them fight a desperate defense of the complex against increasingly challenging enemies or something. You need to give your reader an idea where you're going with this, because otherwise it just looks like you're lumping big names from Gundam together for no other reason but doing just that.