This always rankled me as well. Part of this no doubt stems from the philosophy of "realism" implied and underlying the system as a whole. TFT used a sensible and logical system to provide the mechanical basis for playing an adventure game. My own preference for heroic, over super heroic, game play is a clear design element of Heroes & Other Worlds, and is based on what I saw in the foundations of the original system.
Somewhere, so it seems to me, the ability to increase skills instead of attributes became an unavailable option in TFT. As both Melee & Wizard allowed only attribute increases in their rules, and as they served as the foundation stones for the Fantasy Trip, it seems logical that only attribute increases with experience would carry through. I disagreed with this and the result is the experience system in Heroes & Other Worlds.