Thanks for those considerations Andy. When me and Mitch played we noted the following:-
Dice roll for commander traits, some types (Aggressive) would be unlikley to be chosen.
Limit infantry armour piercing to one or two small unit 'tank killer' types.
Limit the number of larger squards in a force- maybe 1 per 18pts (like vehicles).
Allow pinned units to do something if they recover (even if its just going to ground) as otherwise they risk being shot, pinned, rally, shot, pinned , rally etc.
The stun option doesn't make any thematic sense at all.
No psychic species (ie auto psychic action pass)
Restrict some of the Psychic powers (esp visions of terror).
The way the rules are set there seems little point taking the militia rabble.
I think there was something about medic as well but can't remember that one.