The one you max first is often the ability you use the most. Let's look at this guy: 
Consider these two possibilities for your first 8 skill points.
Q-E-W-Q-Q-R-Q-E
or
Q-E-W-Q-E-R-Q-Q
Practically the same, except that you take a second point in E at level 5 instead of level 8, so that your skills aren't so lopsided. The difference is that during levels 5, 6, and 7, your Q is 1 level below what it would normally be, and your E is 1 level above what it would normally be.
About how long does it take to get from level 5 to level 8? About how many times do you think you use Q during that time? Like 20 or 25? And about how many times do you use E during that time? Like 5 or 6? Is it worth giving up 40 damage (total on 2 hits) on all 25 of those Qs for being one rank behind, just to get an extra 30 damage on all 6 of those Es for being one rank ahead?
Now apply that same formula to the rest of the game, and to a truly even skill distribution. You'll be slinging like 100 weak-ass Qs from levels 5 to 15 just so that your 20 Ws and 20 Es will be stronger.