The biggest problem is with binary resists and how they interact with spells, especially crowd-control spells and other debuffs. Any character that casts spells (basically, everyone except warriors, although rogues can get away with the occasional poison resist) is forced to devote a large portion of their item budget to spell penetration in order to have reliable CC, which is especially costly early in an expansion since most resistances seen in PvP are passive/active buffs that scale with level.
Binary resists differ from melee avoidance in that they cannot be avoided by attacking from behind; when my Maim or Bash is parried, I have either been outplayed or was taking a desperate attempt from the front. When my Cyclone or Entangling Roots is resisted, I was merely out-RNGed or failed to stack enough spell penetration (as a physical dps).
This issue can be solved without making resists useless; in fact, I believe they can be made a more reliable and interesting mechanic to gear into. Resists should negate a flat percentage of direct damage (of a given school) and reduce the duration of spell debuffs by a flat percentage (again, of the relevant school). This would make stacking resistance of a given school useful for protecting against PvE burst (you will know how much "effective spell health" you have) and remove the RNG aspect of resistance from PvP while maintaining their usefulness against both damage and debuffs. Mage Armor could have its infamous passive duration reduction removed; the resistance would provide a similar (although probably shorter) duration reduction as a function of spell resistance.