Yeah, I guess it depends. I have 32 point buy, 3/4 max hp, most splat books allowed, half the party is using Tome of Battle, I buffed the martial classes a bit... so my game's more high powered than some, although I do ban/nerf plenty of caster goodies, too. I do also have 5 players now (early on it was as low as 3, though) and Torrent as a player-controlled NPC (re-built as a Crusader / Cleric / "Pearl Knight Vindicator", which is just a swimming-based variant of the hide-oriented Ruby KV). Still, the classed NPCs often have terrible AC and saves, are under-equipped for their listed CR (I understand w/ all the humanoid foes, treasure hauls are a concern, but w/o that gear, they're not really the listed CR), and multiclassed spellcasters seldom seem to have the "non-associated levels" factor into their CR calculation. As it is, I think the CR calculations for class levels are a bit too high in 3E, at least after the first few levels. I've largely adopted a policy that PC non-caster classes and adepts are their level -1 for CR; PC caster classes are CR = level, and NPC classes (other than adept) are their level -2 for CR. If they're under-equipped, that might also warrant another HD to make up for it.
The Inquisitors are rather easy targets, yes. I've actually tried to buff their defenses and make them more support-oriented b/c my players beeline for them as it is and they usually die within 2 rounds of combat. They then proceed to nearly die to the "mooks," who I've buffed offensively to encourage the party to whittle them down first rather than focus firing the inquisitor. Clearly, I need to do more to keep the Inquisitors alive longer... All Inquisitors now generally have levels in the Church Inquisitor prestige class (I adapted it to be LE instead of LG) and my
homebrew vow of poverty, so they can have good defenses without giving up that savage look. My VoP rule is also available to the PCs, but I mostly consider it a godsend to let me properly equip a portion of the NPCs w/o giving the party outrageous wealth. I guess the tattoomancy can fill that role to an extent, too.
Serrimus doesn't need to be nor should be a serious threat, but I think Sorc 3 for some more 1st level spells and Practiced Spellcaster to make his CL worthwhile is a good choice, and calling him "CR 6" as written is really disingenuous.
I don't mean get rid of the level drain on the Tragedies, just to be clear. I mean give them a sonic attack to mix in with it so they're not JUST level draining every turn.
Not sure if you finished the chapter yet, but I added a detail to the end that I thought I read originally, but I guess my mind filled it in...
[sblock]I had the King, as the reality of all he had done / allowed to happen hit him, attempt to commit suicide due to being overcome with the grief. The party got a chance to stop it and just barely succeeded (it was amusing how much the dice wanted him to die, though). I thought it made sense and added some powerful drama, and helped make the king more sympathetic, especially since early in the chapter the players hated him so much they were considering trying to overthrow him. After that, they felt bad for him, and he was deeply grateful to them.
If you want the mechanics I used...it was basically a sense motive check for everyone in the room (Duke Gallo made it as well as some PCs), success meant getting to roll initiative with the king to try and stop him. Unfortunately, the king rolled really high initiative and the few PCs and Gallo that beat him all failed their disarm/grapple attempts. It came down to the PC w/ special visions of the future (an aspect I've greatly expanded upon in my game with actual in-battle mechanics to retcon bad stuff as "visions of the future" to a limited extent) to grant another PC a chance to stop him that finally succeeded.[/sblock]