I write them to be dramatically correct, not by the book. I am always impressed how some people, such as John Cooper, care so much about the correctness of the stat block. I may admire his work but I don't think it is necessary. I don't care much about the stats as long as they sound good for my purposes.
Writing a NPC has little to do with skill points and number of allowed feats. Writing a NPC is all about the right stats to do whatever the DM thinks is dramatically appropriated to that character.
I usually choose a level, take note of the saving throws and BAB, which I immediately adjust to what I think it would be necessary (if necessary, I calculate latter the abilities). I write the hit points taking in account the level of the character and the story need (sometimes I adjust it during play), choose some feats I think would be cool, sometimes I write a couple of skills that might be useful and, when needed, I choose some spells to be prepared (leaving a few to improvisation). Finally, I equip the NPC based in whatever is needed often anticipating the impact after the players take the loot. Characters like this are usually with some unspent skill points and feats, while magic books are still open to be defined. Still, players will rarely notice any difference to BtB NPC. With practice, you just write it in a couple of minutes and it is ready to go.
