I like to suggest the idea of a non-linear skill system with the option of selecting specific fields you can specialize in, or just go your own way and create a character from scratch. (I took the time to simplify this so it takes less time to read.) These are ideas, nothing more, nothing less.

Mechanical Tree
Use(bonus)/Repair/Manipulate/Control/Rewire/Bypass/Disarm - Anything mechanical & anolog technology
Modify/Customize/Invent/Craft/Create/Build (requires tools/parts/items) - Mechanical usable items/equipment, modify mechanical weapons, create surgically installed mechanical enhancements, complex/mechanical explosives (make bombs/traps/mines/missiles/rockets/RPGs/throwables), vehicles, machinery, mots, etc
Tools Needed - Multi-tools, tool kits/sets, tool boxes, tool benches
Bonuses Blunt & mechanical weapons, learn more from NPC's (hands on learning), Bonus damage/criticals vs anything mechanical & mechanical suits, better luck finding mechanical parts/devices.
Special Abilities - Extra aiming options for immobilizing mechanical enemies, can build/modify/customize vehicles for traveling

Science Tree
Use(bonus)/Repair/Hack/Reprogram/Rewire/Bypass/Disarm - Anything computerized & anolog technology
Modify/Customize/Invent/Craft/Create/Build (requires tools/parts/items) - Computerized usable items/equipment, modify computerized weapons, create drugs and medicine of any kind, create surgically installed biological/computerized enhancements, chemical/computerized warfare (make bombs/traps/mines/missiles/rockets/RPGs/throwables),
Tools Needed - Laptops, PDA's, mobile phones, chemistry sets (different sizes/grades, more advanced are smaller & computerized)
Bonuses - Chemical & computerized weapons, reading comprehension, more damage/criticals/accuracy vs enemies with computerized parts, better luck finding chemicals and computerized parts/devices.
Special Abilities - Extra aiming options for immobilizing enemies with computerized parts

Survivalist Tree
Extra Sensory Perception/Survival Skills - Sees farther ahead on travel map, advanced warning for enemy placement on travel map, better party placement when encountering enemies, can hear approaching enemies, can spot injured/crippled enemies without extra perks/gadgets/enhancements.
Invent/Craft/Create/Build (requires tools/parts/items) - create basic medicines, make clever/simplistic/explosive/poisonous bombs/traps/mines/throwables
Tools Needed - Knives, Multi-tools, tool kits/sets
Bonuses - Bartering, stealth, traveling speed (for entire party), dodging enemy attacks, reduced radiation/chemical damage, spotting traps/hidden enemies, better at finding anything usable by any character, much better luck finding keys/key cards/passwords/maps/information.
Special Abilities - Can overhear private NPC/enemy conversations for information & secrets, knows when an NPC/Enemy is try to manipulate/lie/cheat/steal.

If you read through, you'll see that every character type can make it by them self through a game without help from another player, but can still benefit by playing with other players. Certain abilities are also shared between each tree. And after you master one field, you can choose to train in another or tweak it as you go along with the non-linear skill system.

Anyway, thats the kind of system I'd like to see. Yeah sorry, I didn't mean for that to be so long.