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Tobold Pretty sure that's exactly what Imaculata meant, it's just his first sentence was a typo.
It's not exactly a typo, what I meant was that there's a difference between the base challenge rating, and the actual challenge that an enemy is to the players. I would not adjust the CR itself based on his selection of spells, simply because the game assumes that a spellcaster would have a decent variety of spells (both direct damage and not) at his disposal. But of course you can make an estimate whether he is below the CR or above it slightly. Just know that it is not an exact science.
It all depends on how you play the wizard. A wizard with stinking cloud can be just as dangerous as a wizard with fireball, depending on how you use him. That is where the muscle comes in to protect the wizard. A wizard that has mostly damage spells, and relies purely on that, will find himself in a bit of trouble once the muscle of the party gangs up on him. Good luck casting spells when a barbarian is smacking you on the head with a sword every round. Wizards don't exactly have a lot of tanking potential.
But place the wizard with stinking cloud on a good vantage point, with some other enemies to keep the players off him, and suddenly that stinking cloud can become a big problem. And I think that is a point that you already covered pretty well.
What I would do, is make an estimate of what the players are likely to do once they encounter him, and how the wizard is going to respond to that. What are your players strengths and weaknesses?
-Do they have a lot of melee power? Then better place the wizard somewhere hard to reach, with bodyguards, and maybe even make him one CR higher. You could even give him spells that weaken their melee potential.
-Are they weak on magical defenses? Then maybe exploit this weakness, and use spells that they'll have a hard time dealing with, such as ongoing effects.
-Are they strong on magical defenses? Then have your wizard bring dispell magic. He might have to deal with some of the spells that the players throw at him.
-Are they strong with ranged attacks? Then maybe have the wizard bring spells that shield him from projectiles, or put him in a spot where he has cover.
-Are they weak of will? Then hit them with illusion spells, and watch them struggle. As in the example I gave earlier, the party can't reach the wizard, if an illusion makes them think he is out of reach.