Well I think there are a few things that are important with how aliens+UF should work out
1. Alien attitude should be important, if you make the aliens red, they should cause you actual problems (mass pillaging, capturing units, cities, or just tying down a defensive force) on all your border areas (at any part of the game)... If the aliens are green, they should still cause you some problems in the border, but not significant ones.
2. Aliens should not be a 'random kill' in the early game (krakens wandering across a sea city)
3. The UF should be important in handling them, enough to help, but not enough to render them unimportant
4. The quest should make a difference and be balanced
So...
Alien behavior
Blue..don't attack anything, your units bump them out of the way, UF doesn't affect them
Green..Non-collosals attack your units + tiles occasionally (more often near their nests, less often near your city), colossals only attack units within 2 range of a nest
Orange..all aliens attack your units + tiles often (more often near their nests, less often near your city), all aliens attack your city Occasionally
Red..attack your units, tiles, + cities Always (they only back off to wait for reinforcements)
Alien power...
scales up throughout the game somehow (so that by late game Colossal aliens are matches for ultimate units)..ideally due to your units
Base Effects of UF
Orange aliens don't attack your city
City defense bonus v. aliens attacking your city (red ones)
Quest Bonus
Green+Orange don't attack for radius 2 around this city
Combat Bonus v. aliens to city attacks and all units in range 2 around this city
OR
Green+Orange don't attack trade units From this city
Aliens that Do attack Trade units from this city take X damage (red ones)
If the boost wasn't too big, and alien power scaled up enough, then those would be significant choices.
Assuming keeping the aliens at blue was also difficult and involved actual costs.