Part 2 of the issue: Rewarding synergy.
Suppose someone wants to make a Shaolin Space Monk.
They will pack in Mysticism, Martial Arts, Armed Combat (let's pretend the two are split as they were previously), Dodge, and presumably Conversation, to teach their flock.
Given 20 points for skills, this means they will have ~4 points to go into each ability, which goes roughly: 1, 1, 2 for each, leaving them with 3 in each skill.
Meanwhile, another character is built optimally, giving themselves Conversation, Dodge, and Armed Combat (with 2 points in Mysticism for the exp bonus from that one shrine in that one place). With the same 20 points, they have: 1, 1, 2, 3, leaving them with 4 in Armed Combat, Dodge and ~Conversation.
Now, the game being the way it is, having a well-rounded Monk with both melee skills is a total waste - you'll fight unarmed maybe twice ever, armed combat is and will always be better, and you could have spent those Body-stat skill points on something else. Effectively playing a well-rounded character is punished, roleplaying is punished.
The solution I would propose is synergy talents.
Essentially these would be a free "talent" (as the simplest way of handling it as close to the existing system as possible). If you have 5 points in X - Martial Artist for example, then you receive a +1 bonus in another skill, perhaps several other skills. If you have 10 points, you receive a further +1 bonus and so on.
This also helps maintain "expected" skill levels with the above proposition's skill capping.
For example:
5 points in 1st skill > +1 bonus in 2nd skill's rolls
Reflex
Mecha Gunnery > Mecha Artillery
Mecha Piloting
Mecha Weapons > Mecha Fighting
Small Arms > Heavy Artillery
Body
Armed Combat > Martial Arts
Martial Arts > Dodge, Armed Combat, Spot Weakness (living target only)
Toughness > Athletics, Concentration
Athletics > Toughness, Initiative
Speed
Dodge
Initiative
Mecha Fighting > Mecha Piloting
Stealth > Awareness
Perception
Awareness > Stealth
Heavy Weapons > Small Arms
Insight > Awareness, Spot Weakness, Shopping
Spot Weakness
Mecha Artillery > Mecha Guns
Craft
Code Breaking > Electronic Warfare
Electronic Warfare
Repair > Mecha Engineering
Survival > Stealth, Toughness, Stamina, Awareness,
Ego
Cybertech > Medicine
Intimidation > Taunt
Mysticism > Martial Arts, Concentration, Conversation
Concentration > Mysticism, Repair, Medicine
Knowledge
Biotechnology > Medicine, Science, Cybertech
Mecha Engineering > Repair, Spot Weakness (Mecha Only?)
Medicine > Spot Weakness (living only), Biotechnology, Cybertech,
Science > Biotechnology, Medicine, Cybertech
Charm
Conversation > Taunt, Intimidate
Performance > Concentration, Taunt, Intimidate,
Shopping > Conversation, Insight
Taunt > Intimidate, Conversation
At 5 points, this is compensation for not specialising (since for the same Exp investment you could have just got an extra few points in the skill), but at ten points in a skill, a +1 bonus from 5 in another skill works out cheaper and lends itself to a more rounded, "real" character (and gives weak skills an easy boost).
This also alleviates a possible downfall of the above suggestion - the mechanical uselessness of the generalist. Where someone making the absolute most of the system could sink all their reflex points into Mecha Pilotting and get 20 in the skill, another player could put 5 into each of the other three skills as well, meaning they had a much harder time than the specialist.
With a synergy bonus system, a mecha specialist could cover all five mecha skills and pick up a series of bonuses that would alleviate the later exp penalty, whilst still allowing the specialist to have an advantage of their own.
Disclaimer: All Skills and figures mentioned in this thread are perfectly changeable to fit balance considerations, they are provided as examples and for demonstration of concept only.