At least one person following this thread agrees with you! I think this is an excellent rhetorical point which has not really been addressed by the defenders of fly.
Because the points have been addressed over and over. A combat spell with different levels of damage is a decision of equilizing the power of the spell for it's level. A 1d10 fireball and a 10d10 fireball are both fine, but one is higher level.
Flight was removed in favor of a tactical version of flight. It is a once per day affair and is not useful for long distance flying. It's not just the Fly spell, a flying carpet can only hover slightly above the ground. Teleport is the travel option now, which of course eliminates all the encounters in between, rather than just bypassing some.
Part of the problem also, is the rule against having more than 1 of the same power memorized for a Wizard. If I'm walking around Sharn, I can still only keep one Feather Fall on me at a time.
As for points that are not addressed by "the opposition", I haven't seen much discussion about the teleport answer to flight's "problem", just as everyone glossed over the 3.5e design decision of ADDING flight in tons of places.
If freeform flight was such a problem for 3e, then why give the warlock unending flight? Sure the entire party isn't flying, but then the combat advantage really only applies to a caster/ missile attack guy.
(I had a dragon riding gnome in 3.5, charging and meleeing meant flight's advantage was reduced. It still gave me some advantages of course, but since things aren't free, that power came from somewhere.)