Lockpicking should be turned into the "infiltration" skill, remove Hacking from the Science skill, add in the Lockpick kits of the first 2 games, add in a bunch of other uses for item either crafting items and such. Leave the Minigame for characters with low lockpick skills (and restrict their access to lockpicking the more advanced doors) while the high level players just go around with their auto lockpicking kits and viruses that only they can craft.
There's a lot you could do with reworking the skills plan. Here's what I personally think would work:
- Add a new skill for "Marksmanship" or something like that, because aiming a laser rifle and aiming a hunting rifle aren't that different.
- Combine "Guns", part of "Repair", and Lockpicking into "Mechanical" a skill that measures how facile you are with simple mechanical devices like guns and locks.
- Combine "Energy Weapons", the other part of "Repair" and "Science" into "Science" a skill that measures how facile you are with high tech devices.
This way you could keep the 25/50/75/100 thresholds for bypassing security because the other levels of the skill will do something.
Then you could have your skills be Barter, Explosives/thrown, Marksmanship, Mechanical, Medicine, Melee, Science, Sneak, Speech, Survival, and Unarmed. I think 10 is the minimum number of skills for a good Fallout-ey system, but 13 would be better so invent two new mechanics and make those skills.
EDIT: I suppose you could make a "Heavy Weapons" skill distinct from marksmanship that serves the same purpose (determining accuracy, and critrate say) since aiming a missile launcher is sort of fundamentally different from aiming a rifle.