1. There's no guarantee that there was an Aeon ACU even on that planet. From the looks of just the communication and the skirmish in the intro, Rhiza was only overseeing the entire battle. Possibly from an HQ elsewhere in the galaxy.
2. When you look from above, the ship is indeed red. But several close-ups show some blue plating as well. Considering the fact that all faction-specific ACUs are piloted by their respective faction-specific commanders, it's likely that the ship is still UEF. Also, the design isn't as spiky as the other Cybran designs (for example the ship in the Cybran intro in SupCom). Yes, it's not as blocky as the ship in the general intro of Supcom, but the design feels much more UEF than Cybran to me.
3. It was definitely a Seraphim ACU rather than an Ythota. It also probably was an overcharged shot. An OC killing an ACU is still more likely than a normal shot killing an ACU. Ad
4. Clarke probably have gotten out if she recalled immediately, like Dostya. She insists on shooting some more and then being shot at, after the recall of Dostya. That changes some things. If recall was impossible right away, just walk away, through the maze of buildings.
5. Here's an improved version, in which dotswarlock gave a good insight in how the game mechanics would work in the more story-like situation:
https://docs.google.com/file/d/0B_LpCNQ9Qch-eE5TbU4tODI5Y2s/edit?pli=1.
As always, the balance of a game doesn't hold up with the balance of a story or the balance of real-life. If we had an FPS, in which a standard current-time army rifle would be as deadly as it is in real life, many people would be fed up quickly, with instant-kills everywhere. A quick google search tells you that some British WWI artillery had a range of ~10km. Those things certainly weren't as large as the T2 static artillery, which can't fire 10km away.
Finding the balance in a game and then finding a plausible explanation in the story isn't that easy, but I think dots has written it quite well. Anyway: in book 9, he tells more about that ship, which is definitely UEF for him. In book 10, he gave a reasonable explanation as to why Clarke didn't recall. In book 6, he gives a nice explanation as to how the Seraphim could manage to OC ACUs in a single shot (though this would be in the past at the time of the botched ship evacuation mission). Book 6 is called "broken balance" for a reason
I'd recommend reading book 1 first and working your way through it. Then you can get accustomed to the characters, otherwise, you may get a bit of trouble in the later books (you'll get in trouble anyway, if you try to make sense of Bagby...).
Flynn wrote:We can only hope that she perished in the ACU explosion
It's an ACU explosion. A thermonuclear explosion right under your cockpit. I don't think you'd survive that. You should be happy if you're destroyed at a molecular level, rather than an atomic level.