Agreed on #1-5.
My main worry with Pellaeon is that he will be bored with our spec-ops mission profile, and he might be requested to come to Central HQ to help coordinate TG's greater strategies and battlefleets. If we can keep him, great, but it's not a priority.
As for the Al'Kesh, yes, I agree with trying to keep them. They're great as dropships, since they can cloak and they have Ring Transporters, and they can provide close air support.
The Indefatigable was performing those duties earlier, but I think we can agree that it's better to have the Inde telebombing/sending over away teams to capture enemy capital ships.
Keep in mind that one of the Al'Kesh is currently functioning as an Omega Trap and keeping a S.U.E. Alucard in stasis.
If we package up the design plans of the modifications that were done to the Al'Kesh and the Indefatigable's phaser array, we should be able to get some concessions from HQ. I mean, we just found a way of neutralizing extreme supernatural S.U.E.'s somewhat easily and without danger to TG agents. Not to mention, since this would be carried out by two cloaked star ships, all the locals would see is the Great Beast being sucked up into heaven, and they can praise their gods for deliverance, repairing the Canon quite handily.
I think the SCV's proved their usefulness in setting up a defense, and their ability to repair vehicles and machines alongside the Antaeus 01's repair Scarabs, should make keeping our force in fighting shape much easier.
I don't think we need to keep all 12 of them, but maybe 2 or 3 would be nice.
Also, let's try to keep the Blaster Bomb launchers and a supply of Blaster Bombs from the X-COM squad if we can't keep them.
Guided mini-nukes are ALWAYS welcome. And if we have access to an X-COM Apocalypse or Interceptor Canon, we can purchase synthetic Elerium-115 for making more blaster bombs.