It strikes me as interesting that climb and swim have skills that govern them in terms of skill and speed, but land movement, burrowing, and flying do not. I think that each speed should have a skill that determines how fast one can move and with what skill.
Climb and swim work as written. Burrow should operate in basically the same way.
Each character should have a base speed, but Run should allow him to move faster and should be used in places of relative speed, such as races or rushing to escape before the mummy's tomb collapses. Possibly, the base speed should be eliminated and speed be entirely governed by Run checks.
Given that a fly skill exists, perhaps it should replace the jump skill. Not only would the combined skill (I'll call it Fly) govern flying maneuverability, but at low values, it would also govern jumping distance and accuracy. With a high enough skill check, actual flying should be possible. My reasoning here is that, given a mid to high level game, if an enemy or ally spellcaster casts Fly, the melee-focused fighter is useless. Foghter-types approach obsolescence as their levels rise; this would help to alleviate some of that.
I'm not sure why the Fly skill isn't governed by the new Acrobatics Skill. The Fly Skill doesn't give you the ability to fly -- only the ability to maneuver, dodge and weave while flying from other means. That would appear to be a function of acrobatics.
My suggestion was that the Fly skill actually give the ability to fly.