Thief AKA Pickpocket

this hasnt realy been discussed much other than "it needs to be changed", here are the stats for them

Synergies
+2 modifier to Slight of Hand Mundane Skill
+1 modifier to Stealth Mundane Skill
+1 modifier to Parry Mundane Skill
+1 modifier to Counter Weapon Skill
-2 to Ranged (base) HUD stat
-3 to Melee (base) HUD stat

right, too point out, Counter (one of their bonuses) is being counteracted by that -3 melee (in other words, +1 parry skill, but that -3 melee makes that bonus into a -2 Counter) the only thing i can think of for this is to allow players to select from a set list of skill and have a max of +5/-5 in synergys

Personally I think that each base class should have a list of skills that can be picked to have an advantage or disadvantage in, since not all player examples of a class are carbon copy.
I think the +5 -5 system was a reasonable way of balancing, though I think the option to have a variable total of Advantage and Disadvatage, as long as it isn't min-maxing to the extreeme should also be allowed. Obviously a character should have equal advantages and disadvantages.
Below are my suggestions for possible selectable advantages (disadvantages would likely depend on the character concept).

Fighter: Physical Attribute/Caps, Acrobatics, Balance, Charge, Parry, Power Attack, Melee Weapon Skills
Pickpocket: DEX, SWA, MAN, Acrobatics, Aim, Distract, Dual Weild, Slight of Hand, Stealth, One-Handed Melee Weapons, Ranged Weapons
Guardian: STR, PHY, Balance, Distract, Parry, Power Attack
Scout: DEX, KNO, SWA, Artillery, Craft_, Distract, Focus, Lore_, Medical, Perception, Stealth, Ranged Weapons
Mercenary: Any
Tradesman: KNO, SWA, MAN, Chant, Diplomacy, ESP, Focus, Lore_, Medical, Music, Magic Skills

Note that I'm rounding out general roles. Fighter: Melee expert, Pickpocket: Ranged/Light Melee Weapons, Scout: Ranged, Tradesman: Magic. My only concerns are that I couldn't think of many skills that Guardian would viably have an advantage in without possibly branching too wide, also that Mercenary should have some skills they can't have a bonus in even if they are the Jack-of-all-trades.

yeah though dont forget to take into consideration that certain classes have higher hp, which gives classes like traders (+6 hp, and taking into consideration fighters +10 hp or guardians +12hp) a realy bad disadvantage, perhapes also a system where the lower hp starting classses get more skill points for the start (since the hp + is accumulative with each level you gain untill you change to your advance class)