Sometimes aircraft used on certain routes have a poorer seat pitch than those used on other routes of the same airline. The code-sharing partnerships between groups of airlines mean that the airline you book with may well not be the same as the airline you fly with. Even within the same class on the same plane the seat pitch may vary, with the best seat pitches usually being nearer the front. The comments are my own. United 32 inches Virgin 34 inches Reported as being less than this on their Florida flights As well as seat pitch, the seat width can also vary, with planes of the same type operated by some airlines having more seats across each row than those of other airlines.
Many charter flights take off and land at very awkward times of the day.
In-flight comfort factors such as the seat pitch and the number of seats across each row tend to be considerably less favourable with charter airlines. In the event of problems, charter airlines do not tend to have the same level of backup facilities that scheduled airlines have. I believe that with some charter airlines you may not be able to make seat reservations in advance. They also often provide consistent flight timings allowing for convenient changes between airlines in the same alliance, together with baggage transfer handled by the airlines rather than passengers. However, the likely effect of less competition on prices is worrying.