Ok, sure. But, is that a problem with the CR system, or a problem with this specific monster? I'd say it's this specific monster really. The CR system is working the way it should, but, this particular critter is bad. So, fix the critter - which is apparently what they're doing by switching away from caster slots.
I think I may have lost the thread of the conversation somewhere because I'm not seeing the problem.
It's probably a problem with the CR system. I've made a lot of monsters--well, converted them from older editions--and glass canons and glass tanks are
everywhere. Unfortunately, the way determining CR works often lends itself to these sort of imbalances
and generally disregards abilities that aren't directly related to either defense or inflicting damage. You could give a pixie the ability to spam
wish spells and by RAW it really wouldn't affect their CR, because
wish does not, by itself, affect AC or damage. More realistically, though, CR calculations don't take non-damaging spells and SLAs into account, no matter how much they could affect the encounter, and they don't take things like stat-drain into account, which is why shadows are so very under-CRed.
The "easy" way to fix it would be to make CR so that creatures have to have the same CR for both offense and defense
and to include every ability in the calculations.