Okay. I'll tentatively assign polywell fusion reactor(s) as the power system. Though some secondary system power schemes might run better on other generators.
As far as i know, inertial containment fusion reactors are more interesting for small scale, while continuous reactor designs are better for big ones. Though polywell is not the only possibility there, tokamak is the most common example and should scale just as well. Heck, even some technobabble like weber uses (gravity containment something) would be possible. The interesting point here is that starting fusion needs quite a lot of energy, so when you want a large power output over a long period of time, it's the better choice to leave the fusion process running continuously, as opposed to fusing small pellets of fuel repeatedly.
The ion drive would do best with a dedicated generator, right? Then you wouldn't have to run through all that power re-routing crap that's so popular in scifi, like on star trek. Not that I'm holding up Star Trek as a useful example for a hard sci-fi system.
That's probably best asked of an electrical engineer with some experience in high power systems, but as far as i'm aware there's no problem with having a single reactor powering everything. Though a very useful feature of such a reactor would be to have variable power output, that shouldn't be a problem for a sufficiently advanced fusion reactor. It should be able to function with various levels of fuel input, and thus various levels of energy output (and heat generation).
As far as i know, "power rerouting" is just so much bullshit anyway. You can't expect of any normal type of machinery to work better if you just pump more energy into it. Most would burn out instead. Or at least blow the fuses.
And if you don't have enough electricity to run everything that's hooked up to your generator/battery/power outlet, you usually deal by simply switching one off.
Though some (smaller) backup power systems can be sensible for other practical purposes. For example starting a fusion reactor would require quite a bit of energy. So you'd want at least some good capacitors to store enough for that. And you'd probably also want to be able to run life support independently, in case there's some problem with the main reactor that is still repairable but takes time.
The best choices i can see here are either capacitors, which would need to be a lot more efficient than the ones we have today, though even now there's research into that so i'd call it plausible speculation to have really good capacitors. Or, second choice, fission reactor. The advantage of those is that they're pretty foolproof, require refueling only every few dozen years, and are safe. Toshiba currently has some designs in testing that could provide 200kw for around 40 years and is about 24m³ in size. Would be perfect for running lifesupport on a ship whenever the fusion reactor is powered down. Though that assumes pretty big ships already, for a small sized ship, a simple fossil-fuel powered generator might be the best choice, though miniaturization might be the most reliably predictable of all technological advances.
BTW, what are the major dangers of this sort of fusion reactor?
Not a lot of dangers really. Fusion reactors of all kinds do not explode. Since the big problem in getting them to run is to actually contain the fuel so that fusion can happen, any major damage will cause the fusion to fizzle out resulting in no explosion whatsoever. If whatever type of containment happens to be switched off abruptly (magnetic in tokamak, electrostatic in polywell) you still have a big ball of hot plasma though. Which will immediatly expand, burn anything in it's path, while slowly getting colder. But if you have decently thick walls around the room where the reactor is placed, it should only damage what's inside. Heck, you probably have enough radiation shielding around such a reactor anyway.
The reactor "overheating" or some such thing, as often seen on StarTrek, is also not a big problem. If it's decently designed, it should be possible to switch off the fuel to the reactor with the press of a single button, making the plasma ball go *fzzt* almost immediately. Obviously, you'd design such a system with many redundancies. Heck, you could even have a simple manual valve on the fuel lines somewhere, in case absolutely everything else fails and you need to switch it off.
Depending on what fuel is used for fusion that might be volatile. The easiest type of fusion is with hydrogen isotopes, which means hydrogen tanks on board. The cleanest type of fusion would be boron-proton, still requiring some hydrogen tanks, and lot better containment, since the plasma needs to be about 12 times as energetic for the fusion to start. "Cleanest" because it releases a lot less harmful radiaton than deuterium fusion. Which is the biggest hazard of fusion reactors, most types of fusion release neutrons and gamma rays, which will turn most materials they hit into radioactive isotopes with varying half-lifes. So after some time, pretty much every part of the machinery exposed to the fusion plasma will be highly radioactive. Not a problem in space, just chuck it in the nearest sun and replace the parts, but people definitly shouldn't walk around inside the (switched off) reactor without protection.
