Them graphs, the ones to do with resist points to be exact, look as they would follow neatly along with how much your points are worth. What I mean by this is: The "bumps and lumps" you speak of are the curve changing when you start to have to spend 2/3/5 points in a resist instead of 1. The mitigation doesn't go up by 2/3/5 times but the curve does increase some what at them points, what suggests to me it's intentional.
The armor it's self might be different though, I don't think the resist points should be changed by looking at that though. I fear if we try and make this game totally linear it will loose some of it's charm and be heading toward every other mmo out there, what means i might as well go play planet side 2.
By all means fix bugs and exploits and make the game run better and in a more balanced fashion. Just because the resist profile is a bit more complex then a straight line, doesn't mean it should be changed. If however there are balancing issues with classes and armor, then yeah this should be addressed.
Tanks are supposed to be hard to kill, it's what that class is all about, spys are supposed to take f all dmg and die fast. But like you say, they do need strengths and weaknesses in all classes that make them more balanced, without totally trashing any class and making the broked ones playable again.