Wait, meaning that while it's technically possible, but it'd be really tricky to accomplish? Gee, I wish I had written something like "Branching would be really tricky, but there's no physical barriers" at the top of my post ;)
Well, there are physical barriers to a static design that allows branching. Actively moving an entire section of tube to reconnect it to a new one is sort of a brute-force approach, and highly unlikely that it would be worth the complexity and risk, in my opinion at least.
Drag is reduced in the first place by using hydrogen even at a given pressure. And you can use 1/4th the pressure and still maintain lift because you're moving four times as fast. And given how few reboosts are needed from LA to SF in the base case, a few more per unit distance hardly seems limiting.
1/4th the pressure is still problematic, because what do you do while you're accelerating up to speed? You'd have to use pressurized onboard gas to levitate with, which would then require more vacuum pumping with every run. The Alpha design uses wheels for "taxiing" at low speeds; it's unclear at what speed the compressor is able to provide all of the needed lift.
If you consider that the steel Hyperloop pipe draped across 30m-spaced pylons will approximate a vertical sine wave, then at 700mph the allowable sag is only about 5cm
Irrelevant because earthquakes impose far more deflection that you have to be able to counter (and that the proposal calls for countering) than a craft moving past.
Relevant because the problem is the frequency, not the amplitude. Large earthquakes tend to cause much lower-frequency deflections, which are far easier to deal with, even if the amplitude is higher. The problem I described has to do with the static height profile of the tube, not the effect of the passing capsule distorting it (which is negligible). Even if the skis (on springs) can accelerate at 10g's to maintain contact with the tube surface, then a 5cm oscillation with 30m wavelength is sufficient to cause the skis to completely lift off the surface of the tube after each pylon, causing a very jarring ride. A low-frequency earthquake deflection on the other hand, say with 200m wavelength, could not realistically have high enough amplitude to cause the skis to skip like this. Of course, if you have the bad luck to be riding the hyperloop straight over the epicenter when the earthquake lets loose, then there will be high-amplitude earthquake waves of all frequencies and all bets are off.
Mechanical braking from 1500mph in the event of an emergency is also a non-starter
What, you're picturing drum brakes or something? You're moving at high speeds in a giant steel tube. Magnetic braking couldn't possibly be easier.
The Alpha proposal calls for a "mechanical braking system"; I agree that magnetic brakes would be preferable in principle, though at Hyperloop speeds there's enough kinetic energy involved that the capsule component of the brakes would likely melt from the induced current. Permanent magnets on the capsule would probably be too heavy. And magnets/electromagnets on 350 linear miles of tube would likely be too costly/complicated. So unless there's a way to have the electromagnet component on the capsule, but make sure that nearly all the heat is dissipated in the steel tube and not the capsule, I'm not sure it would be workable. I have similar concerns about the aluminum capsule rotor, and whether it might become problematically hot during the linear acceleration/deceleration phase. A solid aluminum rotor could absorb the electromagnetically induced waste heat from 0-700mph acceleration without melting (by a factor of about 2), but the Alpha design calls for it to be hollow. And accelerating to 1500mph involves >4x the energy of 700mph.
a 700mph capsule will incur about 2g's of aerobraking deceleration
Where are you getting this from? Even if the tube was instantly full pressure (which it wouldn't be), a streamlined shape will not experience 2Gs at 700mph, any more than a passenger jet losing full engine power does. And anyway, 10g horizontal is not fatal even if that was the case. The average untrained individual, properly restrained, can tolerate 10g for a minute without even loss of cognitive function.
According to High-G training, untrained individuals tend to black out between 4 and 6 g's. (Then a few sentences later it says that one minute at 15g's could be deadly, then a few sentences after that says that several minutes at 17g's is ok. Go figure.) In any case, streamlined passenger jets are not traveling 700mph in 1atm; more like 550mph in 0.2atm. And the Hyperloop capsule is emphatically NOT streamlined; it has a honking circular front cross-section with a giant compressor on it, designed for very low-pressure input, which would immediately stop working if the pressure spikes up. Subjecting the entire Hyperloop capsule shape suddenly to 1atm, in a tube not much bigger than it is, would result in tremendous aerodynamic drag.