I also agree with pretty much all your points. We all take umbrage with SC3 for obvious reasons, but my favorite part of it was definitely the voice acting. The voices in the enhanced 3DO version of SC2 were primarily the development team at Toys For Bob! And while they were a creative group, they definitely weren't professional voice actors, but I have a feeling that was due largely to Accolade's budgetary constraints rather than a lack of creativity on their behalf. All of the SC3 voices were really individualized and had great comedic timing and personality. It was really the only aspect of the game that kept me wanting to play, because the gameplay or sense of adventure sure wasn't anything to look forward to. Niffiwan alone was utterly hysterical and a reason to keep playing.

I agree with the Mycon backstory idea too. Some of the interference with the canon really went too far into the absurd as to be comically insulting (e.g. devolved Precursor cows) but the Mycon plot was a clever take on the material. On the other hand, the insidious plot of the Arilou to use humanity to sustain their species also seemed like a big step in the wrong direction. I always felt the Arilou had more noble ambitions and grander cosmic agendas to tend to, rather than to be plotting a grand conspiracy to use humans as some kind of genetic broodmares for the preservation of their race.

With regard to the Xchagger, I also thought it was a brilliant idea and opened up the concept of introducing other races of varying scale and size. Why stop at the very small though? Why not have some aliens the size of whales, or bigger still? Maybe a race so physically large that their ships dwarf those of other races? They wouldn't necessarily have to be more powerful, just bigger. The Sa-Matra is a good example, although it obviously had incredibly powerful defenses. It would be nice to see more of that idea though: defeating large enemy ships that require strategic attacks from multiple ships to take them down due to their large size. This could even serve as a springboard for an interesting multiplayer co-op mode, I think. Having alien ships of various size would be a more realistic gameplay dynamic than having all the aliens and starships be roughly the same size and scale.

I think SC3's idea of an area-spanning coalition of very different species was an inspired idea. Sure, the Hegemonic Crux was built on lies and corruption, but when you get down to brass tacks, the only races in SC2 that were completely on board with joining the New Alliance Of Free Stars without any sort of pre-membership errand were the Orz and the Pkunk. Everybody else was fine with the player saving their skin from the Ur-Quan..."provided you take care of a little problem, know what I'm saying'?"

As much as I loathed that HAL-9000 wanna-be League Ethics Complaint Management System in SC3, it would have been interesting to see how many of the decisions in SC2 would have raised the Alliance's collective moral ire under different circumstances. Consider the following:

- The Spathi needed the player to commit an act of genocide prior to temporarily joining up.

- Any deal with the Druuge involving the slave trade.

- Using a hyper-wave caster to impersonate the Ilwrath deities, leading to an act of mass-genocide that wiped out the Ilwrath and Thriddash species.

- Interference in the religious practices of the Pkunk (via Quija board). 

- Providing cryogenically frozen female Shofixti to a sexually depraved ("I will wake them gently, then commit unrivaled acts of fertility!") individual.

- Inciting the Yehat civil war.

- Detonating a weapon of mass destruction (Utwig Bomb).

- Unwilling genetic(?) manipulation in a species evolutionary cycle (Chmmr).

The list goes on and on; depending on your point of view. Now I'm not advocating a return of that goddamn red eyeball of pointless interference, but it would be nice to see how the player's actions affect his/her standing or reputation in the galactic community. I would also like to see consequences; such as races joining or leaving the Alliance/League based on player action.