Originally, Hover was meant to be "combat flight", which is why it sacrifices speed for defense, and why it can be slotted for both flight speed and defense. Fly was meant to be the out of combat travel power, and it sacrifices speed for mobility (all 3 spatial axes). In fact, Fly used to have a movement suppression effect if you attacked while Fly was active: they took that out only recently. Afterburner was added much later, towards the end of the original game's life, and it's sole purpose is to boost the travel speed, which is why it suppresses combat powers entirely.
Super Jump and Super Speed also used to have suppression features to discourage their use in combat, so it's only a recent development that these could be used in combat. They are faster than Fly because they sacrifice some mobility. SJ gives you the Z-axis, but with limited control over trajectory, SS gives you horizontal speed, but no Z-axis (unless combined with CJ, SJ, or one of the prestige sprints). These kinds of trade-offs are "by design" -- they're features, not bugs. *shrug*