I will start with a couple:
People running their engine at the pumps for ages, holding everybody up, before they move away. This is driven by schools charging for brakes-off to brakes-on.
People turning into wind for engine checks, doing a 180 to do that and then doing another 180 to get to the runway. This is pointless unless the engine is actually overheating. Again, PPL training teaches this dumb practice.
People complaining about how bad it all is, when it is the biggest joy of my life.
That I agree with.
The first also happens in different setups, where people are charged differently.
The reason is more that once the engine is running the average student or 10-hours a year pilot is totally overwhelmed by operating the aircraft, running religiously through that (too long) written checklist etc. that the world outside of his own aircraft simply dispappears.
The second, I think, is mostly a UK fetish. In other parts of Europe, yes, occasionally an instructor will insist on this, but most don‘t. Except in very hot condtions, I’d say an engine which overheats during idle on the ground isn‘t right.
Then there is the famous three-sixty in order to check for traffic, but again, that‘s a little weird IMHO. When I am about the line up, the only traffic I am interested in that which is on final or maybe just about to turn final. That‘s it.
Having to PPR airfields that see 5 aircraft per day.
Waiting for some unforecasted mist to lift up, while changing plans every hour with passengers waiting.
Instructors leaving their plane empty at the fuel pump between 2 training flights (the FI apologized, so I forgive him 
)
Needless hassle or complication does annoy me. Probably the biggest is the lack of flexibility (some may say common sense) if one wants to operate slightly outside of the perceived box.
Most of it fades away once in the air and able to enjoy just flying and looking out the window.
Airports which require PPR/Slots and deny flights when the quota is full despite ample capacity.
Beautiful weather outside and no time to use it…
People not smiling at the fuel pump ;)
Most irritating? For me, that this thing is really flying.
Airfields with short opening hours, and not allowing you to simply fly in and out when the office is closed.
The use of the phrase “third country” – as originated by small minded people who think being obtuse is clever.
