It's an interesting assumption that the letter has to mean something. Given that there is very little meaning in numbers, what is to say the inclusion of a letter always has a meaning, and indeed, always has the same meaning!
We've seen an example above, where Stagecoach Oxfordshire used 'S' for 'Superior', yet many counties (by no means all) have spent the last year using 'S' as a prefix for Scholars only.
To take the all stops X78 example above, what would have been the assumption had First decided to number it F78, or even Y78?
It's the same with suffixes - West Midlands has that use of an "E" suffix (for Exception, IIRC?)... does the uninitiated ask what happened to the A, B, C and D variants of the route, because surely to have an E you need the others to have got that high?
Whilst there is no doubt a letter prefix or suffix often has a meaning, we should be wary of immediately associating the same meaning to that prefix for every operator, everywhere.