Guess I'm one of the 1 in 400's for reading the entire post ^_^
OP +1!
There's a bunch of really nice ideas in your OP, many of which will not only enhance the 'staying power' of SWTOR but also the level of immersion IMHO.
I'm liking the idea of squadron space missions / invasion fleets, they would add a really nice component to the (so far) rather boring solo space flight missions, for resource/latency purposes I would suggest keeping them on rails however and not 'free flight'.
I'm all for ghosting companions, even though they are not anywhere near as good as a real player, it might give the side with less people a fighting chance. I suggest unghosting even if the group is full with 4 players to prevent groups having to split up just to get their companions to unghost.
Like some of the other posters said, I also feel that any bonus (even tiny ones) to 1 faction for controlling assets can and will be felt like a detriment by the other side.
It's a fact that some servers have a really really screwed up player balance of rep vs imp.
I don't like losing, or being on the losing side/faction, and I think most people feel the same way, hence I will switch sides if the imbalance becomes too great.
Give both sides incentives to participate and try their best, rewards of some kind, be it titles, commendations, resources whatever.
Here's another idea: invert bonusses/rewards!
The less planets/assets a side has under their control, the bigger the immaterial bonusses to things like stats/exp/war hero titles/buffs but less rewards of the material kind, like crafting resources/commendations/gear.
The more planets/assets a side has under their control, vice versa.
Just some random thoughts, I'd like hear yours about them though
Regards,
E