I have ran the Astromundi Cluster twice as a single-sphere campaign setting and have run into some of the same problems (beefs) that others are seeing. Here are some of the ideas that I used.
I consider the Illithid population to be the population of the Illithid Empire (within the cluster). That includes (free-willed) Varans and slave populations. I put the actual illithid population at about 20% of that. I also have Oortlings (Polyhedron or SJR2) as a "cattle" race the illithids keep in farm colonies. With an internal food source, the illithids are not forced to hunt (and irritate) the other human/humanoid races that they trade with (as much).
The illithids outright lie about their biology and origin. That is to spread mis-information to their enemies and calm the more neive Varans (and other humans they trade with). They also lie about the Illithid Empire's population. "If you're not intelligent enough to discern the truth, then you do not deserve it."
The main advantage the Antilans have over the Illithids is that in SJ, if you destroy the ship at range, all the personal combat abilites in the worlds won't do you a bit of good. That's what the Crystal ships are for.
I also keep the Illithids off balance with a private civil war. The priests of Lugribossk are trying to control the Empire. That would relegate the mind-pools to just glorified breeding tanks. The mind-pools are greatly opposed to this.
I beef up the Antilan's Sun Mages to Fire Elementalists and throw in many of the spells common to the Red Wizards of Thay (hey, I run SJ not FR but have all this material. Plus I see simularities in the cultures). I also introduce Living Masks to the higher level sun mages. Treat them as Vizier's Turbans from the Monstrous Compendium Annual Vol. Two (Al-Qadim setting).
I attribute the large quantity of asteroids and earth bodies in the sphere not just to the two cataclysums, but subsequent gates to the elemental planes of earth, air, and water. The Antilans are responsible for much of this.
The Antilans also learn to deal with the Illithids in other ways. The use of shock troops (slave thri-kreen and wemics given potions to make them resistant to psionic attacks and turned loose on the illithid ships). The use of Priestess's of Gelanicus helps. I used Drow Priestesses of Lolth as a model for these. The Calidian Hidden create a brain posion that causes brain damage, but kills any illithids that consumes the tainted brain.
The native elves have two reasons not to leave. They live in fortress worlds. Avarien and Giltiond are living plant worlds that are almost impossible to attack, even with a large fleet. Couple that with elven magic and ships (don't forget the Doombats) and you have a position you can always fall back to. I treat the Astromundi elves as immune to psionic contact. You just cannot get a contact lock on their minds. Other psionics are possible. The second reason they have to stay is economic. Other races can find ways to exit the sphere, but with out a large number of living ships, they don't do if often. The elves have become very rich and use that wealth to control some political issues. I treat the need for living ships to exit as the "worst keep secret" of the sphere.
The Arcane were difficult to deal with. I finally split them into several groups. Arcane are aware of others of their race that are in danger, but may not agree with them or even like them. So I have many different factions of Arcane. Only some are trying to sell the sphere, only some treat their employees as dirt. You get all kinds of arcane, just as you get all kinds of humans.
I have always thought the dohwar to be just plain silly. I have made efforts to make them more interesting, but still don't use them much. I also wrote them up as a possible player character race.
The Thoric do have some mages, by the way. They are golden eyed (I think that was in the material) and I give them lots of bards (skalds). There are two Thoric priesthoods also; Hordent (Thor) and Yul (Hades).
I see the Calidians much like the Bajorans from DS9. They have been beaten up by just about everyone (mostly by the Illithids) and are trying to recover, but keep running into other problems.
I use the revised S&P version of psionics to keep it a little more even with magic. I liked the idea of lizard-men psionicists also and increased their populations.
The neogi were the hardest thing for me to get used to. Peace-keeping neogi??? Well, greed is a wonderful motivation and I treat them somewhat like a meaner Ferangi. Mojo from Marvel Comics (an X-men foe) was also a good inpseration for a villanous entrepreneur.
I changed the ships around a little bit. I added a couple ships from the web and other souces to the Antilans. Since there are now free thri-kreen in AC, the elves have adopted the leafship. The Illithid allied Varans commonly use the Squidship and Leechship (they look nice with the nautiloids).
I wished they had included more maps in the boxed set. I photocopied the Planetary display pages and created a smaller map of the sphere as a player handout. I also have a copy with color coded special encounters such as large sections of infinity fine, dead space, dark space (undead havens where they cannot be turned), permanent wrinkles (labled so I know which ones connect), and wild zones.
