Yes, you can still partly counter it with ready actions; but a character built around spring attack will likely have a more powerful single attack in mind when building the character - the spring attacker can utilize their specialty (whatever that is), while the opponent does not gain a full attack against the spring attacker. In that sense, it does not get less useful after level 6, because while you're denying yourself a full attack, you're also denying the enemy a full attack.
Flyby attack is likely made the way it is because the designers didn't, at the time of writing Flyby Attack, think very many PCs would be capable of permanent flight. Flyby Attack is much superior to both Spring Attack and Shot on the Run, as it allows any standard action to be performed in the middle of a move, such as Book of 9 Swords maneuver, a spell, an Awesome Blow (a favourite of dragons), etc. It is basically a monster feat (as evidenced by its location), so it may be that the designers didn't think very hard on how it would work if a PC took it.