Armor mods? Coolness factor? Concepts that don't involve minmaxing the best armor rating you can get?
Some things you can put in Milspec armor that you can't do with a Lined coat, for instance:
Strength Enhancement - Does not count against your augmented max. Start with a troll, add muscle replacement, and give him a claymore. See where I'm going here?
Ruthenium Polymer Coating - Same as with a Chameleon Suit, except much heavier armor.
Chemical Seal - Perfect for when you don't want to deal with toxins spraying in the air.
Vision mods built into the helmet - Ultrasound, etc.
Implant weapons in the armor - Cyberspurs, and other fun things.
In other words, STOCK milspec armor is far too noticable for most situations, true, but when you start customizing it, you can get fun things.
Plus, I have a former Red Samurai who kept his old armor when he escaped the SCIRE.