I think of a system like this:
- One floting-point number representing overall skill (maybe with building skill counted as a part of overall skill number)
- Every hit inflicted to building or player should be evaluated for skill value and put into queue of skill claims with inflicted damage, when the building or player dies, the queue will be passed through and claims will be assigned to attackers up to the maximum health of dead player/building (any skill claims beyond maximum health will be cancelled and partial skill claims - like 10hp claim with 5hp remaining to max health - will be adjusted to fit max health). Simply, if you let the enemy heal/repair, you don't get your skill.
- When an alien egg dies, it's skill claim list will be compacted (skill claim list will be truncated to maximum health of egg and all skill claims of each player will be added together) and copied to a special creep claim list of all alien buildings within creep range. When some building loses creep and starts losing health, lost health will be added as skill claims with NULL attacker. These claims will be divided among all players in special list of creep claims. The same will be for human buildings that get powered down (with repeaters and reactor instead of eggs), but aliens get skill for the period of time those buildings stay powered down.
- Builder gets skill points for repairing buildings (humans only, the amount should be equivalent to skill claims cancelled but attackers don't lose skill), every use of building (every player that spawns in a telenode or egg, every item bought at armory, every evo point spent while OM exists, every assigned skill claim by turret etc. and some extra points for every building staying up and running. Builder gets points only for buildings he personally built even after he gets a weapon and goes fighting.
- Builders lose skill for time without reactor/overmind (there should be enough time to rebuild reactor/OM without any penalty - no penalty for well planned move). If the reactor/OM is destroyed by enemy, equivalent of skill lost by builder is divided among attackers.
- When a building or player dies, skill claims will be added to attackers' skill number and substracted from skill of the dead player/builder of destroyed building.
- Winners should get some extra skill, losers should lose a little, no skill gain or loss for stalemate.
- General modifiers of skill claims: team balance (team player count ratio), skill balance (victim/attacker skill ratio, only for PvP hit, not against buildings), attacker's equipment, victim's equipment (inverted), number of turrets in active range (even blocked ones).
- Alien evo modifiers:
Granger - 2
Advanced Granger - 1.5
Dretch - 1
Basilisk - 0.9
Advanced Basilisk - 0.8
Marauder - 0.7
Dragoon - 0.6
Advanced Marauder - 0.5
Advanced Dragoon - 0.4
Tyrant - 0.3
Human modifiers:
Builder/unarmed (only blaster) - 2
Soldier with blaster - 1.5
Rifle, no armor - 1

Lucifer cannon, battlesuit - 0.3
This means if you slaughter grangers with lucifer in battlesuit, you get almost nothing but if you kill tyrant with blaster on your own as unarmored builder, you get lots of skill points.