A capstone that supports the Challenge ability instead of Supreme Charge. Bump Supreme Charge down two levels, and give them the ability to Challenge without flanking or something.
A one-point Evolution to change your creature's type to Undead, Ooze, or whatever.
A somewhat bigger spell list (alleviated because you can in fact apply Spell-Like Ability mutation to yourself).
Evolutions to apply templates (half-fiend, half-dragon) to the creature.
More support, more alchemical items alleviating this handily.
The ability to brew potions. Learning new extracts. Better use of alchemical items.
More discoveries, at more levels - they don't do enough to restrict them 1 every 4 and they screw you up bad if you don't focus on a single path.
Better mutagens and extracts. A larger list of extracts.
Research journal.
Golem-creation, chimera-making, and maybe a few nods to Fullmetal Alchemist's Alchemy flavor without actually -making- it a transmuter would be pretty neat.
Lead to gold without wasting a discovery. Seriously.
Mix-n-match bomb elements. Lightning-Smoke, Electro-Flame, Sonic Fireball, whatever. Why can't we do this? What -possible- use is there to limit it? Half damage to one, half to the other.
More mutagen effects. If you're that concerned about Mutagens being overpowered, tweak them at least so they can stack with Extracts.
Higher-level Extracts. Form of the Dragon I is the best we get? Really?
Give 'em Smite. Pick a guy, go to town on him with HOLY/UNHOLY SMITING POWERS, wail until dead. Rinse, repeat.
Failing that, I'd prefer to see some sort of Justice power set up like an inverse Rage - pick debuffs, trigger them on the target, wail on him until he dies. Rinse, repeat. Call it Supernatural and function for (Rage rounds + Wisdom Modifier). Maybe call it "Torment" - certainly Torture is a classic of the Inquisition.
Tactical Feats are a bad way to show off a new feature that should've been with the Cavalier from go. Don't do that. This is a class whose name evokes "Inquisition" - destroying your confidence, beating you down, and holding your head under the water until you talk.
Give them some form of Detect Lies. You're an Inquisitor. Inquisit. (Yes, I know that's not a real word)
Give them some tracking bonuses. Who cares if it's too close to the Ranger? Rangers aren't the be-all end-all of trackers. Heck, make it magical tracking - tag a suspect, tail him through shadows, and find the Den of Iniquity, bust down the door, and go, well, Spanish Inquisition on their collective butts.
Rename Judgement. -Please-. Call it "Faith," "Holy Strength," "Divine Power," whatever, but Judgement is so not the name for something that buffs you. English language + Game synergy = good! Game - English language = gibberish.
Either drop spells, or make their spell list more aggressive. While Inquisitors have a nice spell list, they are not thematic at all, and the new classes are seriously saturated with buffers and self-buffers. Give a little blasting to a class whose name forces to mind images of guys in robes carrying torches around.
Magical debuffing would go a long way towards making me feel less like "this is c+p divine bard" and more like "this is a freaking Inquisitor."
Torment: An Alternative To Unfocused Class Abilities
Torment (Su): The Inquisitor must face down all manner of heretics and demons, but that doesn't mean he has to do so on their terms. A canny inquisitor wields his faith not merely as his shield but his sword, stripping away the advantages of his monstrous and heretical foes with merciless resolve and putting them one by one to the judgement of his god.
An Inquisitor may activate a Torment as a move action. Each Torment affects a 1+Inquisitor's Wisdom targets until tenth level; at tenth level, Torments expand as the Inquisitor's faith has been proven in the fight against his god's foes, enabling him to affect twice this number.
Flensing: The Inquisitor strips away his foe's resistances with the strength of his god, clutching his (un)holy symbol and thrusting it at his foes to force them to feel his patron's wrath. The target's Damage Reduction, Energy Resistances, or Spell Resistances (choose one) are stripped away by a rate of 1 point per Inquisitor's Charisma. At tenth level, the Inquisitor may choose two effects; at twentieth level, all three apply.
Wrath: The Inquisitor wields his wrath as a holy weapon, calling down the rage of his god to deal 1d6+Charisma damage to a his targets in punishing retribution. This damage increases to 1d8 at level 5, 1d10 at level 10, 1d12 at level 15, and 2d6 at level 20.
Terror: Presenting his holy symbol to his foes, the Inquisitor calls his god's anger to strike the fear of the divine into their heathen hearts. Targets must make a DC (10+1/2 Inquisitor Level + Charisma) will save or become shaken. (Improves as the others do at 10th and 20th level, I just don't have my books right now).