I don't mean to bump, but I wonder if anyone else had these issues yet:
I went through Aquarius today on 3.6.14 RC6 (not 7 yet), and I had two red alert screw-ups:
1. First Contact, you're supposed to have a Pegasus. I warped into the next mission and was in an Aurora.
2 (not as bad, but still): Universal Truth, I was flying a Perseus with a Prom-S/Kayser, Harpoons and Trebs, only to come in Journey's End with a Prom-S/HL-7 and only one Harpoon bank (all my missiles were depleted, and I magically get 16 Harps). Oh, and Gamma 4 was marked dead (I wonder if it's because before the Banishment Conversation, all non-Alpha fighters depart?).
Surprisingly, in Universal Truth, I made Gamma Ares and Ursas with cluster warheads (since the AI cannot fire the Trebuchet by default), they did a frighteningly competent job and survived for about three fourths of the mission on Medium.