With regards to the train throughput is almost always linked to the number of trains or capacity of the ride. Not enough results in low throughput. Too much on a coaster can also harm throughput though. However, in Drayton's case I think it's that they simply don't get enough in the first place. G-Force would be definitely improved with a second train though.
Think about it. Train 1 loads > Train 1 dispatches > Train 1 hits the SkyLoop > Train 2 has parked by now > Train 2 down loads > Train 2 begins to load.
While train 2 is loading train 1 is still traveling around the track. Even if the ride stacks slightly you are still in essence loading twice as many people in one go (When it stacks) One full on leaves and as it does another one enters, ready to be loaded. It is short, so the staff would need to be well trained and effective to try and not stack. It would be challenging, but it could possibly be done. The X-Car trains aren't very big. The only real change I think would be good to make is reprogram the ride system so it can hold one train at the base of the lift if the other hasn't cleared the brake run by the time the first is there. Kind of like how Air slows down when the main circuit isn't empty (Though obviously, given the nature of the lift it'd be better to hold it at the base rather than travel slowly and potentially need to stop in an awkward position).
As for Shockwave, changing the trains for B&M ones would be very expensive, as no doubt given it's age B&M would have to specially make them. That wouldn't come cheap. However, I heard rumors that when the trains were overhauled recently they did use some B&M or B&M compatible parts, due to the originals being either unobtainable or expensive.
There are ways they could speed up Shockwave too though. All they need to do is add a video and some signs in the second half of the queueline explaining how to board the ride (Think like Duel does). That's one of the most common things I see when in that station. People simply can't grasp how the restraint system works, so have to wait for a ride host to help them. By doing this they'd give people a bit of pre-warning, and it wouldn't be too expensive to produce and implement. It could easily all be done in house.
If they did that, and had the staff running more effectively they'd be much better off. I have wondered if Drayton have any structure for their throughputs on larger rides. A lot of big parks set their ride teams targets they have to reach each day. If Drayton don't do this it's something they would be wise to consider in my opinion. If the staff simply can't be bothered to adhere to it then all they need is some incentive to do it. Even if it's something simple like at the end of the season the ride/attraction team which has consistently been on target are rewarded in some form.
Like I say, I don't know if Drayton have such a system or not, but if they don't it's something to consider. If they do then maybe it's time they clamped down on it.
There are lots of little things the park could do to try and increase throughputs though. Hopefully, with this new attraction we'll see something which can hit at least 1000pph. I do wonder if that is part of the issue (With Shockwave anyway). When the park installed certain larger attractions they didn't anticipate the gate figures they would be getting in the future, so rather than planning ahead with throughputs they just went for the easiest solution. I'm sure when Towers installed Nemmy they didn't think they'd really need 1400pph at the time, but these days it sets the benchmark for their attractions