I think the biggest problem at this point is the fact that unless you really know what you're doing (usually involving cross-referencing several websites which carry the relevant information), it is extraordinarily hard to sort through fare classes and select one over another, even on an airline website. Handy example is Virgin Atlantic, which offers "Lowest" or "Flexible" for Economy, Premium Economy, and Upper Class (e.g. Business Class). Well, unless I use a specialist website like ITA Matrix I have no way of knowing whether "Lowest" is actually eligible to upgrade or not, for example. Ditto Travelocity and so on. I use Virgin Atlantic as a handy example but I find this sort of situation is rather common.
Given market demands, it would be nice if there were at least a standardization of various fare classes across carriers (e.g. so an "N" fare on United would get the same rights/privileges for changes, upgrades, and as one on Delta), with the "un-standardized" fares being clearly listed as such and passengers being able to specify at all purchase venues which class they wanted (presuming availability) across all legs and carriers. Oh, wait, that would be painfully like pre-deregulation practices...