It kind of feels like I am talking past a couple of posters here.
In my opinion, milspec armor belongs in military adventures not something to be found in your average Shadowrun.
Still my opinion, at the point where I see armor stacking get out of hand (and this is GM taste) I will give the player an OOC "really, that seems like a good idea to you?" Should they persist, they might get a random traffic stop by the Star (yeah, it may not be PC to profile but my cops at Lone Star do), a heat wave (if the time of year is appropriate), and so forth. Normally, it doesn't take too long for the message to sink in.
The point of keeping milspec armor in a certain range of protection is game balance (because the designers know that if it exists it is probably going to make its way into a situation where it doesn't really fit), if the only way to take out a guy wearing it is with an assault cannon things get skewed really fast.