The way I understand the changes in skills available runs like this:

Combat skills[list][*]Shotgun Proficiency
[*]SMG Proficiency
[*]Pistol Proficiency
[*]Assault Rifles Proficiency
[*]Martial Arts Proficiency[/list]
Physical Skills[list][*]Stealth
[*]Toughness[/list]
Technical Skills[list][*]Tech Savvy/Hacking
[*]Gadgetry
[*]Conversationalist/Psychology
[*]Medical Knowledge[/list]

I'd suggest adding 'Athletics' to the Physical Skills set, to differentiate it from Stealth, which should then give [@Avanhelsing] the option to make a stealthy character who can get in anywhere while not being combat orientated. If you classed Lockpicking as a Stealth ability rather than a Tech Savvy one this would also help.

Making Patch Athletic/Tech might be worthwhile too, since he wouldn't be able to sneak around much, but would be able to climb in though a second storey window if required. :)