Reposting from the Announcement thread on the FP Roundtable:
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Version One:
Create a special Skill Tree that you can only earn points for in Faction Play. The tree is the same for everyone, as are the number of skill points awarded per FP match (varying by wins and match score). However for Loyalists, certain branches of the tree will be cheaper for a particular faction. Thus, there is no imbalance in the long run, it's just easier to build up in a certain direction in the short run.
Version Two:
As above, except certain portions of the Faction Play Skill Tree are only available to faction Loyalists. Any points spent on faction exclusive skills are lost if you leave the faction. This has more flavor, but could create balance concerns.
Here are some ideas for Faction Play related bonuses:
Satellite Uplink -- For each player with this skill on your side, increase the duration of Satellite Sweep by 1 second
Jamming Repeater -- For each player with this skill on your side, increase the duration of ECM Sweep by 1 second
Capture Acceleration -- 'nuff said
Dropship Firepower -- Increase damage of dropship lasers on the dropship your mech arrives in
Anti-Emplacement Weapons -- Increased damage versus gates, turrets, gens, the radio trucks in domination, etc.
General bonuses:
Good Maintenance -- Reduced chance that enemy fire will cause a critical hit (possibly broken up by locations or equipment types)
Rapid Air Support -- shorter delay on air strike arrival
Dedicated Artillery -- shorter delay on arty strike arrival
UAV Durability -- Increased hit points on your UAV
Faction Bonuses (either cheaper for that faction, or only available for that faction):
Steiner -- Structure bonus
FRR -- Heat dissipation bonus
Kurita -- PPC velocity and laser duration bonus
Davion -- Ballistic velocity and MG ROF bonus
Liao -- Heat capacity bonus
Marik -- Missile reload bonus
Jade Falcon -- Reduced cycle times for SRM, small energy, flamer and LBX
Wolf -- Armor bonus
Smoke Jaguar -- Projectile velocity bonus (all types)
Ghost Bear -- Laser duration & cycle times reduced