Design the BBEG at the CR you want him to be.
If you need him to be 5th level for story reason, but only as strong as say, 3rd level for combat reason, then just design him as if he was really 3rd level. The party isn't going to know what level is actually is. You could just say he is 5th level, but that he is wounded and used some spells already, he is effectively 3rd level.
Honestly, what is the real difference between a wounded 5th level caster out of 3rd level spells, and a 3rd level caster who would have fewer hitpoints and no 3rd level spells? His saves may be a little lower, he has a couple less skill points. Nothing major. (Other then equipment, which the 5th level character would have more of. So just give the 3rd level version more gear then normal.)
I'm writing up a Necromancer for my first level party to take on. I need him to be around 5th level to story wise, do what he is suppose to be doing. Unfortunately, a 5th level wizard is dangerous against a first level party without even a rogue or ranger to get the drop on him. He will certainly hear them coming and have time to prepare.
He will only have 20 HP, his third level spells will be "spent" making the area skeletons that the cleric should chew threw pretty easy. I can make sure he doesn't have any deadly area of effect spells like sleep. All of his feats will be story based - nothing to help in combat with PCs.
What is this guy's CR?
Side question = A skeleton is worth 135 XP. Are they still worth that if a cleric just rolls through and channel kills them all no problem?
I'd apply an Ad-Hoc adjustment to his CR based on how difficult he is in the fight in comparison to a lower level wizard. It's actually not that difficult since you're dealing with a wizard. Compare his spells, Hp, and defenses to what you feel a wizard of a lower CR would posses. If it more or less matches up then you're probably in the correct ballpark. His feats don't really affect CR (but can affect his options and/or his strengths).
If you're really apt to making him inept (denying him AoE 1st level spells even) then you might need to adjust his CR down exorbitantly or even considering him akin to a noncombatant (if he's really weak, has no spells, no defenses other than the skeletons, etc) if the battle is really just about the undead.
Personally, I don't like dumbing encounters down that much. I'd rather have the group face an adept apprentice or something. With one amusing exception. If he has been level-drained (say the necromancer got into a spat with a fledgling vampire) and is sitting with a few negative levels. Then you could definitely toy around with some amusing antics like spells being cast below their usual caster level, such a 7th level wizard with 6 negative levels can cast cone of cold for 1d6 cold damage, or black tentacles that only has a +6 bonus and lasts 1 round.
Post us your 7th level necromancer wizard (5th level wizards cannot cast animate dead) and we can work on adjusting him down to a lower CR. Or if you decide "yikes, he's too low a level, so he must use a wand of animate dead" then you can use an Adept instead who is of the appropriate CR.
5th level wizards can cast Lesser Animate Dead though, if you're just using skeletons and zombies.
Sometimes a lich is a lich. Carving him up into too small of chunks and you're giving them a foe that essentially has its head on the chopping block and the guillotine chord ready to hand out. Liches, dragons, demons, etc...are iconic for a reason. Not because they "give it up" to every player that wanders through the crypt door.
Thematically you could have him be a free-willed awesome undead foe. Just use something more tuned to the character party at hand. Maybe use a Dread Zombie:
Sometimes when the ceremony to create a lich fails, the would-be lich instead becomes a dread zombie, attaining eternal unlife at an unexpected cost—the loss of some of the intelligence it had in life. These undead recognize and mourn their lost mental acuity, and this knowledge translates into a sick hunger for living brains.
Here is a link to the d20 pfsrd in case you don't have the AB in your library. (you should though because it is awesome sauce :-))
Build yourself a wizard NPC of an appropriate challenge rating with Dread Zombie on top. Poof...you have your big bad without taking the "real" fear and deadliness out of an actual Lich.
Ashiel, thanks for the good ideas.
I hadn't written him up yet. Good catch on the spell level. I thought it was a third level spell. I'll post him in a little bit.
Thanks.
Not a problem. Keep in mind that negative levels are a pretty good way (and thematically appropriate depending on the conditions of the story). For example, perhaps the party finds the actual remains of a staked vampire that the necromancer was fighting with not long before the party arrives. Perhaps the necromancer is in no mood to fight and may attempt to simply bribe or convince the PCs to leave, or would be more susceptible to being told to take a hike without fighting, or might even be able to pay he party for helping him cure his negative levels (if the party assists the necromancer instead of killing him, award XP as if they defeated him).
For example. Let's take a 7th level NPC wizard with standard NPC statistics.
HP: 34 (7d6+7); Fort +3, Ref +4, Will +5; Melee +2, Ranged +5; Wizard Spells Prepared (CL 7th): 4th-cone of cold, stoneskin, animate dead; 3rd-slow, halt undead, hold person, stinking cloud; 2nd-false life, hideous laughter, darkness, summon swarm; 1st -chill touch, mage armor, shield, magic missile, protection from evil; 0-detect magic, detect poison, light, acid splash
Naturally this guy would slaughter a 1st level party. However, let's pretend that he managed to cast hold undead on the fledgling vampire just before the vampire was about to finish him off, then staked him as a coup de grace on the following round. Barely living. He failed the save to remove the negative levels due to the horrible save penalty from the negative levels.
So he now looks like...
HP: 4 (7d6+7-30); Fort -3, Ref -2, Will -1; Melee -4, Ranged -1; Wizard Spells Prepared (CL 1st): 4th-cone of cold, stoneskin, animate dead; 3rd-slow, halt undead, hold person, stinking cloud; 2nd-false life, hideous laughter, darkness, summon swarm; 1st -chill touch, mage armor, shield, magic missile, protection from evil; 0-detect magic, detect poison, light, acid splash
This version of the wizard is maybe CR 1-2. Using false life he can get more Hp. Burning some components gives him DR 10/adamantine for 10 points of damage. Most of his spells deal about 1d6 damage or only last 1 round. A good "boss" encounter, though I think if this was the most amusing if the party got to chat with him about the vampire and possibly make a friend. :P
I mean, with 6 negative levels he's probably looking to cut a deal.