Clever Phthisis.

Appealing to my 'list-build' side is usually the best way to convince me. I personally think the Emperor is too cheap for what it does, simply because it is almost always the flagship, and therefore means that characters get to be 50 points cheaper (roughly) when one is using such a vessel.
The Ld bonus is worth roughly about 25 pts, so therefore your Warmaster will be getting 25 points cheaper to keep up with other characters (plus I find characters to be a huge points sink anyways).
As far as your critical hits theory goes, think of it this way; it takes three criticals to take out all your launch bay systems instead of 2.
What else are you taking for upgrades? +2rr and MoK I imagine?
The Despoiler is a lot better at shooting than an Emperor, and its faster, both reasonable trades for +30 points, it loses the +1ld sure. So we can assume that the speed and gunnery of the Despoiler has a value of roughly 50 points.
You can say that the Despoiler has +7eq firepower at 60cm. That's worth 31 points by smotherman, and the remaining 20 could be given to the speed benefit. (a person would probably pay 20 points to up the speed of their emperor.)
You have to remember about the disadvantages that an Emperor has that aren't necessarily in its profile as well. A Despoiler fits in well with a chaos fleet, other than its relatively slow speed, the Emperor however, doesn't have an armored prow which makes it scared to maneuver with the rest of the fleet. Also it has the same problem of slowness, but for it, it can't turn if it has a BM in contact. A BIG DEAL. I've seen players fly Emperors off the table because their opponent kept putting a BM in contact.
On another note, I do agree with you, the Despoiler is particularly lackluster, and I would run some other ship, but it's what we voted for. I do think that it should have an additional turret, as it is a carrier, and they always have 1 more.
As a note my general fleet for chaos (which I rarely play):
Repulsive or Vengeance +Warmaster
Hades
Devestation
2x Murders
Murder +lances
Fill out with Iconoclasts/Infidels
Very Ordinance light, but metagame is a factor when it comes to building fleets. In my group no one goes ordinance heavy ('cept me when playing orks, because you have to without FS) Even the Tau player goes relatively Ord light (swaps for torps on explorers).
Of course the fleets I play most often are Orks and Demiurg, followed by Tau, and then Chaos. I'm currently building an IN fleet for Tartanus.