This is after one playthrough with a stealth pistol char, now playing soldier on hard (1/3 done), so take it with a grain of salt.
AR, Toughness, Technical maxed.
2 levels of Sabotage for Breaking and Entering.
5 levels of Stealth for Master Awareness.
The rest in CQC.
Equips:
Level 3 AR with 4 accuracy/stability mods sacrificing some mag size (thinking of Samuel AR for max benefits to stability, which also negates lower mag size issue.)
Silenced pistol/tranq rounds without skill investment for stealth missions/friendly infiltration missions.
Advanced Utility Armor with all damage resistance mods - 15+10+10+5% damage resistance, +10 endurance, -2 stealth.
Additional armor mods for specific situations:
Ammo Netting to start with more ammo, Printed Circuit mods for easier hacking, Digital Camo mods for easier sneaking.
Level 3 med kits.