Allen containment <- any alien autopsy. Optionally, few autopsies? Aquatoid and Gillman?
MC reader <- any live alien. Optionally, few of them + terrorists?
MC lab <- MC reader + alien learning arrays + medic
MC disruptor <- MC reader + MC lab + alien implanter + navigator/commander
What do you think?
That may be too easy for first three but that should be fine. I do not want to scrutinize the progress to MC lab. MC disruptor, from the other side, should be hard to obtain.
That leaves the question what to do with cloning and cryogenics? Cloning is somewhat easier to obtain from F.S. Cruiser but it is not good to add it as a dependency to M.C. Lab as you may encounter F.S. Cruiser only few months down the road + building the facility + one month of initial training = too late.
Maybe add them as requirement for alien weapon just for fun? Cloning for thermal shock launcher and cryogenics for PWT launcher?
I support this idea in general: "delay" the start of the game slightly before getting sonic, but not make the start of the game excessively difficult or RNG-dependent.
I agree that MC disruptor should certainly come later (you can't use it anyway, until you have been a while in the MC lab). Any single autopsy for the alien containment might be a little bit too easy. That would essentially allow starting down the sonic tree as early as in February, March at the latest. This might be fine, because the gauss weapons stay relevant nonetheless due to other balancing choices. I'd suggest at least aquatoid and gillman (maybe also either tasoth or lobsterman as the third, but that might make it too RNG-dependent). For MC reader, I'd suggest some live alien, for example a squad leader, or possibly either a medic, technician or navigator (a MC-capable alien that is). A terrorist would be alternative, but that would be challenging but not excessively so (similar to grabbing a live deep one terrorist in vanilla; however, now this is a bit more trickier, because you don't get access to alien containment at the start, so you'd have to wish for a manageable terror mission later).
I can't think of a logical dependency for cryogenics and cloning. Maybe you don't need one, or you could add one for building manta/leviathan (currently getting them is rather easy). PWT launcher at least could have extra dependencies, because it is an end-game tech in any case. It would be still be OK to have cloning as a requirement for MC lab (you can manage FS cruisers without MC screening), but that would create a RNG dependency on spotting a FS cruiser in the early game. Without cloning dependency, you'd be almost guaranteed a smooth start into the game (which might be a good idea, to not frustrate the players too much).
Edit: I think a general weakness, similar to vanilla, is that you really need very few alien components and once you have gotten them (and possibly researched them), they are essentially useless junk. This concerns especially ones that are slightly more difficult to get, i.e. implanter, examination room, cryogenics, etc. If you couödn't manufacture those components and you needed them to manufacture something, you'd actually have some reason to go for Artifact site missions or very large ships. Now, once you have already obtained everything you could need, you may want to go there and abort the mission. But not sure if this is worth fixing in this mod, because this would require significant rework (similar to TWoTS, for example).