They really don't resemble Phyrexians much at all other than being mechanical. Phyrexians are nightmarish fusions of metal and flesh which worship brutal efficiency as the ultimate form of perfection and want to convert all other life into themselves in painful and horrific ways. Warforged kinda fall short of that bar.
I agree that there's a definitely interesting dynamic there, though I don't think "elves and such" are played out at all. Personally I can't get past the name "Githyanki", though. It just sounds dumb to me. But I love the idea that they're a race of traumatized victims who've become abusers in turn, and like playing them up as coldly pragmatic villains to contrast with the more theatrical MFs - they won't torture or convert you, they'll just kill everything that moves, take everything of value and burn the rest to the ground to conceal all evidence they were involved. I'm not so fond of the whole faux-space thing Wotco does with the Astral Plane, so I'm not particulalry planning to have my Githi riding around in ships, though I may default to it for lack of a better idea. The most logical reason I can come up with is that it's a way for them to launch invasions from a mobile base so as not to lead anyone back to their city, essentially helping them maintain a cell structure to minimize potential consequences (I figure them to be extremely paranoid and cynical).
The inevitables always bothered me because they're styled as the iconic Lawful outsider-race and they're not outsiders. There are the Formians and Modrons as well, but the Inevitables are the ones that actually uphold Law as a virtue, instead of just being conquerors, so they feel like they should be a better fit for the role of "angels" and "demons" for the LN alignment, but it doesn't work because they're material beings rather than spiritual ones. I know it's kind of a hair-splitty way to look at it, but it just bugs me.
My setting has a great use for the Warforged that isn't at all like their purpose in Eberron. They start out more or less the same way, being designed as a weapon and then becoming sentient - but the reason they become sentient is very explicit and not at all how it happened in Eberron (I know this because Eberron doesn't assume the presence of the subsystem which is critical to their presence in my game).
The thing that bugs me about the celestial races is that demons, devils, and angels are all classic mythic archetypes, and Yugoloths aren't that different from demons and devils...but on the celestial side, right next to actual angels, archons which often look like angels, and Asuras which look like angels with hawk feet, we have the Eladrins, who are sort of like Noble High Faerie Lords but aren't actually called faeries, and the Guardinals who are a bunch of random furries. The Eladrins barely begin to feel like they should fit the role of Incarnations of Chaotic Good, and as a force of Pure Good Untainted By Law or Chaos, the Guardinals leave me almost completely cold. To even make them begin to be interesting to me, I had to expand their fluff a lot to play up the idea that they're derived from shamanic animal fathers and play more into the mythological role of the animal than its actual nature, but at the end of the day it still doesn't really feel like they carry the same weight as a celestial force compared to angels. I kinda wish they'd had Angels, by that name alone, be the NG force and made the archons more abstract-seeming, perhaps resembling Kirby's New Gods or other 70s-comics human-esque omnipotent aliens, or else just had the Inevitables become Good and make them shinier so they could be cosmic beings of justice and righteousness.
(Granted, if all this was done, I might well complain about that and wish it were more like the way it is now; it's always easier to find fault than to accomplish improvement.)