I dont see how this is a bad experience at all.

Re choice of seats, it is well known and advertised by CX that one can choose your seats via Manage my booking 180 days before flight with certain (most) fare classes. If your fare class does not allow advanced seating choice, all passengers can check-in online 48 hours before flight. If you were staying in HK, it would have been very easy to find internet to do this. Even if you were in another country, nowadays, it is very easy within that 48 hours to find a computer for 5 minutes. This would have given you much more choice in seat assignment, not CX fault at all.

Re delays. the initial delay was only 30 minutes, yet CX brought out refreshments for Economy passengers. This is definitly a 5 star gesture.

Re boarding, it is standard for US bound flights to have 2 lines, security and boarding. The fact that the line was long is standard, you are boarding a fully booked 747. The CX staff member may have been trying to put you in the right boarding line. CX board Economy by row numbers as well as having lines for premium passengers and MPO/Oneworld elites.

Planes, especially full ones, are always initially hot before and just after take-off, because of the number of people and because cooling systems have not maxed up yet. Inflight, planes cool rapidly. With regard to the odour from the toilets, this is relativley normal if you sit just infront of the toilet area, and it was likely more odorous to the end of the flight, because near the end of the flight, more people use the toilet, and so the doors open a lot.

Not really a bad experience, a pretty normal one, and you could have made it better with planning. CX did their best in handling the delay.