This mod sounds really exciting! Had a comment regarding the command squad, though: about a year ago, I played a mod that added three or four members to the Force Commander, and it completely gimped his Victory Charge ability. Squad members would get in the way and waste/abort the charge, or the entire squad would get butchered piecemeal due to being strung-out and isolated. Frustrating as all-hell, since that charge was pretty much the mainstay ability for the commander early game.
On a side note, I think it'd be nice to have the scout squad equip whatever Cyrus carries; full sniper, full shotgun, or full bolters.
I'd also agree with the suggestion to keep the marine/scout squads at five, not ten. A lot of the campaign maps have really nasty chokepoints that would bottleneck just a ten man squad, let alone that entire bunch. This would also screw with any attempts to be 'tactical' in your fights.