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.