This comes up a lot, to me whenever there is a player that wants to focus on one thing in the game to make their character untouchable as a GM you just starting using what bypasses that more frequently. The game provides options aplenty to ruin a high soak characters day. Same theory in D&D, if you have someone that constantly uses invisibility I just tell them plan on facing a lot of opponents with Truesight, Blindsight, etc. That generally encourages players to not waste so much effort on being such a flat unrounded character.
Alright, normally I would say Strain is the downfall of high armor characters (a wookie for example) but soak applies to Strain damage (which we also took away and added some custom mods that reduce SHOCK damage, or strain damage from energy weapons) What would be a few things that destroy a heavy soak character in the book though? Cause I know if a NPC has like a pierce of 5, my players will start to throw tables a a bit xD
Bolos, Glop grenades, NPCs with Pressure Point, pretty much anything with the Concussive effect.