Honestly, I think the best way to do the tech tree would be based on ethical alignment. In GC2, you got certain techs based on your ultimate ethical alignment. If you could just implement some new WH 40Kish techs in their place or in addition to those already there, you'd be set. Apart from these particular techs, the rest of the Tech tree should be generic for each race (propulsion systems, weapons, etc).
The Tau would be True Good. The Imperium would be Chaotic (or vice versa with Tau) Good. Eldar are DEFINITELY Neutral. The Orks and Dark Eldar are the very definition of Chaotic Evil. Chaos, Genestealers, and Necs would be Pure Evil.
Just divvy out alignment based tech according to that. I'm not sure if Tech can be differentiated between different Good and Evil alignments (i.e. Chaotic vs Pure in both cases) but I definitely know that Good gets techs that Evil and Neutral don't.
Space Marines, Battle Barges, Exterminatus, and various other distinctly, "Imperial," and defensive techs could be specifically determined by the Imperium's ethical (Good) alignment. Also, in a general kind of way, they could get a drastic advance on ship hit points to make up for the, "flaws," of Imperial tech.
The Tau would get some kind of, "Greater Good," tech that makes their planets impossible (or just incredibly hard) to culturally subvert and some kind of defensive bonus on their star ships.
Eldar (Neutral) would have to get some kind of incredibly advanced weaponry or stealth systems, but a serious logistics penalty (generally) to signify their dwindling numbers.
Orks could generally have like increased production and logistics to signify their constant spawning or something like that.
While I like the idea of Genestealer Cults, I think it would also be a good idea to regulate the Dark Eldar (pirates basically) and Tyranid Hive Fleets to the realm of random events (via Antaran Attack Fleets MoO2, Dread Lords in the DL campaign, or Barbarians in the Civ series).
Necrons and Chaos (Pure Evil) should get some rather nasty evil exclusive weapons systems, a, "Corruption," special tech or influence bonus (for Chaos), and some really high end propulsion techs to signify both races' cannonical edge when it comes to FTL travel.
The Imperium should have the Super Soldiers super ability. The Tau should have Super Diplomats.
Apart from that...I'm out of suggestions. lol