Do you ever get any opportunity to land the aircraft on manual systems, such as no auto-throttles. Seems the modern large aircraft uses auto-throttles during all stages, which could become a trap of players when for what ever reason, they fail and you get left with it.
It really depends on what you call 'manual systems'. 99% of landings are manual, with the autopilot being disconnected at whatever point in the approach appeals. Generally I wait until the landing checklist is complete. That means the aircraft is fully configured, and also means that any go around forced by a configuration issue will already have the autopilot engaged.
The A380 thrust can be controlled manually, but it's rarely done, and never for the fun of it. The levers are quite a reach (for me anyway), are stiff, but also sensitive. It's obvious Airbus designed them to be used following failures, not as a matter of course.
In every Boeing that I've flown, the convention was to disconnect the auto thrust at the same point you disengaged the autopilot (on approach). There is no reason to have the A/T disengaged on departure, even if manually flying.
The auto thrust is never turned off in the cruise unless you have some form of failure. Autopilot is also required to be engaged in RVSM airspace.
In many years of flying Boeings, I saw the A/T fail outright a few times. Individual autopilots could also fail, but I never saw the loss of all three (even in QF30..once some switches were thrown). The flight directors are extremely reliable, and I can't recall an individual failure (and there's three anyway).
Airbus have made design decisions that make the automatics unavailable with various failures. Generally you'll need a double failure to cause a law reversion, which is then likely to take away the automatics as well. I had one of those on my second or third trip after checking out on the 380. An odd pair of failures caused the aircraft to decide that two ADRs were unreliable, which caused a reversion to alternate law II and took away the automatics. It was a PITA, but we still flew to our destination.