1 - Long Range
The long range / melee thing makes like, no sense the way I'm reading it. For example:
If you are trying to shoot someone who is fighting one other person, you have a 1 in 2 chance to hit the intended target. With Marksmanship Prof 2, you have a 2/2 chance (which should be automatic), but if the target is S/M -3, you have a -2/2 (so, 1/2, in effect) chance. But if the OTHER combatant is +6 S/M, then you have a 4/2 chance of hitting your target?
Unless it's more like a weighted chance scenario - like pulling names from a hat. You put a tab in with the name of each target, but targets with + S/M get an extra tab for each level, and vice versa with - S/M, and for each additional level of Marksmanship Proficiency you get an extra tab for the intended target.
But that's like, ridiculously cumbersome to determine in a combat, especially with a system that we know from experience will take hours to resolve large combats even without the additional time needed to determine where a shot into a melee goes. This will NOT play well.
Anything, even Alf's modification, would serve only to make an already obnoxious process take longer. If this is an attempt to simulate realism - why start here - there's plenty else in the system that's unrealistic. If it's a balance thing, doesn't the halving DR cover it?
2 - Throwing Weapons -
For the stacking, I agree with Alf's suggestion. For the range thing, how do we determine range? It is real-world distance, or... what?
3 - Martial Arts - the restriction seems a bit steep (no items other than Neck or General). According to this you could use MA while carrying a 10-gallon drum (General, two-handed) but not a ring (Hand). The traditional restriction of no non-MA Weapons or Armor seems applicable - perhaps adding no non-MA two-handed items.
The point is to keep people from stacking huge Item bonuses on top of the sick, sick bonuses from MA. Of course, no matter what the restriction is, if you can have ANY slot filled and still do MA, you'll have an amulet or a cape of protection, or a 50 Gallon drum of Martial Arts Proficiency or something, so I see the whole excercise as ultimately futile.
4 - Cleaving Weapons -
I think the thresholds are a sufficient balance to the additional damage. Why not change the damage to LIFE modifier to something other than x2, and then bump the OR bonuses into line with the other skills?
5 - Melee Flexibility - maybe make this skill abit more restrictive insofar as what you can wear is concerned. I'd suggest not allowing the user of this skill to wear armor at all (or maybe MA armor).
Melee Flexibility is what, Martial Arts Lite, without the possibility of defending against LR? Whatever the restriction is, it should be less than the restriction on MA.
6 - Shield Parry - I would like to say apply this skill only to SR attacks (as SR weapon skills can be stacked with Focus Attack, but Ranged weapons cannot). A parry is just that - deflecting a melee attack. For LR attacks, a shield is a shield .. you're not deflecting the bullet as it flies thriugh the air, you're standing behind the shield and hoping they don't hit an exposed foot or shoulder.
Well, in the Nexus, you COULD build a shield that blocks against LR - force fields, magic shields, and you're damned straight even in fantasy settings you see shields being used to block or catch bolts and arrows.
Also, there has to be SOME counter to long range attacks. Only MA allows for defense against them, if you drop it from Shield Parry.