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Some things to consider:

Chaos-Esque Anthology has little things coded in over the years like:
Bullet Deceleration in Water (along with trails) (thus you can use water for cover like in real life)
Blood splatter on walls when bullets pass through players (noticed Unreal 97 had this, and Xonotic didn't, so it was coded in).
and various other little niggling details that were noticed as absent and programmed in over the years.

It also has big things like the tons of added weapons, and all the rest that has allready been mentioned.

Xonotic itself could be prone to puritanism: one of the devs wanted to strip out all the player models and replace them with only robots so it is "less violent" (don't think they did it, but it was discussed).
Chaos-Esque doesn't entertain such thoughts.

Xonotic has code churn from time to time when a dev decides to refactor everything in the "right way". Samual did this once, and later some new guys refactored the whole thing again.
Chaos-Esque does not do this. It refines the codebase it has. The machine doesn't care how asthetic ones quakec dialect appears to humans.
(Rewriting codebases for no reason can reintroduce long banished bugs).

You can think of Xonotic as american-christianity: subject to bouts of shakerism and other fads,
while Chaos-Esque Anthology is more listening to the voices of antiquity.

Chaos-Esque Anthology believes in slow, steady, methodical advancement. Like a large gear biting into whatever it is biting into.
Xonotic is more of a ... talk about things... some bouts of revolutionary change... some iconoclasm... and churn in developers.

Chaos-Esque Anthology has one developer. Who listens to no one, who no one talks to.

One of these projects makes more progress than the other.

Now, on the otherhand: Xonotic has a ... (close eyes, savor the moment, breathe in, breathe out)...
Xonotic has a Community.

You can go to Xonotic. You can approach it. You can Talk to it.
There are people you can say hey what is up, how be ist.
You can talk about new features you want, discuss enacting them, have arguments about it.

You cannot do this with Chaos-Esque. I mean, you can talk to a wall.
On the other hand, whatever feature you want in your heart... it has a good chance of simply appearing in Chaos-Esque.
The development model is: force of will. You will it. That desire is tranferred to the heart of the developer. He has the desire to suddenly implement a new feature. That feature is willed into existance.
Many people scoff at this development model saying that it lacks _Communication_, however Chaos-Esque has 185 weapons and Xonotic has 18. Many people go on the Xonotic forum, make a feature request... and unbeknonst to them Chaos-Esque has had this thing for many years (they will never know).


Note: Xonotic (and ofcourse Chaos-Esque) has a way of seperating game types. You could do ./xonotic-executable -game vanilla, and ./xonotic-chaos-esque executable -game chaos
The xonotic player info will be in ./xonotic/vanilla, and chaos' will be in the other folder.
Another-Thing-To-Note: ChaosEsque devs don't run any servers, so don't expect to see it on the server list: you have to create your own session.

You could split the difference and get the best of both worlds: talk to the xonotic people (irc.anynet.org #xonotic #qc #darkplaces , also forum: xonotic.org )
Eventually you could tell them about the gospel of chaos-like-ness. They'll ban you then or delete your thread but it would be good for a pull.

Chaos-Esque would like to have it's Own community site too, and someone to advertise the game... but the dev likes to code and not do community stuff. Perhaps someone will someday come along. If people only knew what the game offered...