I'm not really a story guy, actually, so I don't know that I can help you on that specifically, but I am a rules guy. You have clearly put a tremendous amount of work into this 160 page rulebook. I've collected a set of negative comments from skimming the first 30 pages or so. Please don't take the fact that these comments are negative to be any indication that I think your work is poor -- my hope is that you might find these comments useful, not offensive, and the only reason I'm sticking to areas you might look to for possible improvements is because that's a lot easier and I'm very tired right now.
- Bear in mind that at 1d6 per stat, people have a high chance of getting several very low stats, and this will happen much, much more often than in a D&D style 4d6 discard one system, or even the old style 3d6 system. This is because the probability distribution is linear instead of a bell curve. In a party, you might have one person get totally screwed, and one person get very lucky. This is going to be amplified to the extreme in the Melee and Ranged skills, as a character low in both will be extremely ineffective in combat, while a character high in either will likely be very deadly. Since you can only buy +4 to your stats total as you gain experience, this will never be rectified for a weak character.
- A +1 bonus every two stat levels is done in D&D only for legacy reasons, not because it's a good system. I would strongly suggest ensuring that every level of a stat is equally valuable. If every other level is highly valuable, and the ones in between are just stepping stones, that devalues half the levels. I understand you probably don't want inflation on the skill rolls based on stats, but it will probably improve your system if you can find a way to smooth this out.
- On the other hand, this is contradicted in the statistics section, where it says your skill bonus is twice your character's attribute. Which is correct?
- The scientist's Power of Science ability's first upgrade is underpowered if the interpretation in the statistics section is correct, since it's half as powerful as just upgrading the relevant stat. Even if that's not the case, bear in mind it's probably going to be used mostly for attacks and possibly melee or ranged, since those stats seem to benefit the most from one extra temporary level. Make sure this sort of mass combat buff is what you have in mind thematically for the scientist.
- Appraise is a very specific and limited skill, and as such is likely to be unpopular unless you make a point to get your players cheated in shops regularly. You might consider merging it into a more broadly applicable knowledge skill that would let players roll to glean useful knowledge about items in non-shopping situations as well.
- People generally have a consistent maximum jump distance and can judge whether they can make it or not before attempting the jump. Having people roll to determine if they manage to make a jump seems to break with my expectations based on the real world.
- You might consider opening up the civilian skills to other character classes. Are agents really unable to drive in intense situations? Are mercenaries unable to jump long distances or climb things? Are scientists unable to swim? These seem more like skills everyone should have access to, rather than skills only civilians should have access to. In fact, while I understand that civilians are intended to be the generalists, from the skill list alone it seems like the civilian skills should be available to everyone, and the other skills should be prohibited to civilians, rather than the other way around.
- Most of the scientist's skills seem to be centered around supporting other characters. I would make sure your scientists have fun things to do beyond rolling knowledge checks and healing the other people. Also, keep in mind that the scientist's skills being heavily knowledge based is unlikely to feel useful if you don't have a RP heavy play style.
- A -3 penalty to melee/ranged skill raises the number you have to roll to hit on a d6 by 3, literally reducing the probability of hitting by 50% so that a 67% chance to hit is reduced to a 17% chance to hit. If your skill is 3 or less already, do you now have no chance to hit, or still 1 in 6? Also, bear in mind that while you may not have fired an M16, even someone untrained can still hit things with it without too much trouble -- one of the great military innovations of guns was that even a dumb peasant could shoot them effectively with minimal training. This is up to your world design, but unless you're dealing with grenade launchers or other weapons that aren't just point and shoot, it would stand to reason that future weapon designs wouldn't change this much.
- The Demolitions Expert trait lacks an exp cost and requirements.
- This may not bother you, but I notice that the 8HP requirement on the Die Hard trait is mostly superficial when the minimum endurance is 6. The only way to fail the 8HP and meet the endurance is to have exactly 6 endurance and 1 strength.
- Two Weapon Fighting (with the trait) breaks even over using a single one-handed weapon at exactly 4 melee/ranged skill in your system, and becomes a good investment as your melee/ranged skill increases from there. This isn't a problem, just an FYI to make sure that feels right to you.
- You treat a weapon as two handed if it is over 5 kg, but a fully loaded M16 assault rifle is only 4 kg. I would just stick with common judgment on a case-by-case basis rather than opening things like this up to rules lawyering: if it seems like it should be two handed, it is.
- The Knowledgeable trait is basically a way to pay 50% extra to circumvent the skill cap by one. This is an interesting idea, but make sure the knowledge skills are going to be useful enough in your game that players will want to invest to get their skill up to 6.
- I don't know if this matters to you, but realistically, keep in mind that almost everyone walks around 5 km/h, regardless of how naturally agile they are. If you want to keep it 'real' as far as movement speed is concerned, then unless someone is significantly disabled, they should never have a movement speed half of that, and they should always be able to run much faster than that.
- Finally, to save this from being all negative, I do want to mention that I think the cover save system is quite nice. I much approve of applying a second cover roll to block a successful attack rather than applying a penalty to the attack roll. If I can make any suggestion for it, you might alter it so that the attacker is making the cover rolls (with inverted targets, eg. 2+ to hit instead of 6+ to avoid the hit), so that the proactive party is still making all the rolls.