Here's a thought: Why not use the skill bonuses from the reputation system as 'free' skill points in a way?

Like the Omega Weapons Training to start, it adds 30 to your Weapon Proficiency skill.

Let us say a player had 99 in WP, and got that bonus. So he has 129 points, but as the skills are done in this game, the amount of gain is lessened despite the 30 extra points.

But, what if the player respecced, and only put 5 clicks into WP, which would be 65 points if I am thinking of my skills correctly. Then, the bonus 30 would still apply, giving him 95.

What this means is that the player, losing very very little damage with his weapons, can now take those freed skill points, and put them elsewhere, like...Grenades, or Combat Armor, etc.

So, thoughts on this?