Personally I like the idea of radar stations that someone proposed up-thread. Hex-building that grants recon on surrounding tiles based on level, requiring machines for the first couple of levels and then hitech parts for the remainder.
Radar lv1; 2t radius, 50 recon, tools
Radar lv2; 2t radius, 100 recon, tools
Radar lv3; 3t radius, 125 recon, electronics
Radar lv4; 4t radius, 150 recon, electronics
etc., up to a max of maybe 6t/200 recon, with no stacking of the recon from multiple stations in close proximity, so you still need scout units if you want proper details beyond vague sensor contacts.
Could also tie in to AA units to improve their performance if AA/planes are enabled, but that might just be unnecessary or too fiddly.
Spies, as already noted, are extremely effective against Non-Aligned and some of the minors that lack anti-spy capabilities.
(Don't ask me how a spy manages to "blend in" among Arachnids, does she just put on a spider Halloween costume ? )
I think it's best to think of scouts in minor/indigenous territory as scout/ranger types. Rather than blending in amongst human populations, they're living off the land, using various spotting equipment and portable comms gear to radio back updates on tribe/herd movements.
Most indigenous critters probably won't care as long as the scout doesn't get too close, and for all other circumstances I imagine there's all sorts of neat tricks like pheromone/scent masking and such. Bugs that only hunt by scent? Make yourself smell like one of them!
As for "the remaining forces being too weak to really hold anything", tell that to the poor AI ! :
Now granted, at some point I *did* have to call those 9 tanks -
(now pretty obsolete, but still kicking ass!)
- to slap down the AI in the places where it was massing troops, and where he managed to start to push back my line...
I've noticed the AI can be a bit dumb about engagement and stance use at times, so that might have contributed to the effectiveness of your otherwise obsolete tanks. As it turns out, All Out Attack isn't a very good stance if you're not, you know, actively attacking.