Speed caps were increased not all that long ago. Fly is slower because it has increased functionality as a tradeoff. Afterburner is designed to be a short duration boost. Y'know, like the afterburner on a jet. Afterburner and Evasive Maneuvers (along with their PB counterparts) increase the flight speed cap. The Jump and Steam packs available for free from the START vendor also significantly boost flight speeds and can be stacked with Afterburner.
PBs and WSs have always been a jack of all trades, master of none AT. But they're still fun to play. Stealth IOs, while not full invisibility, make it easy to cruise thru missions.
At one time the cap on Superspeed was set because it was the fastest speed the client could reliably handle. Still might be the case.