I was teaching my little brother how to play D&D the other day, and he asked me why Armor Class and Saving throws were different. (This came up because that was how I explained it to him, that they work similar.) So I asked myself why as well and began playing with numbers.

You make an attack roll.
1d20 + BAB + ability modifier
against a DC of
10 + Reflex save

The difference is a change in BAB. You still have Good, Average, and Poor but the progression has changed.
Good is equal to 2 + 1/2 Levels in a Good BAB class
Average is equal to 1 + 5/12 Levels in a Average BAB class
Poor is equal to 1/3 Levels in a Poor BAB class

These progressions are also used to create an average save bonus.
The average progression was created with the fact that 5/12 is directly between 1/2 and 1/3. The +1 differentiates it at low levels (that was the original purpose of the +2 bonus on good saves, so they were different than poor at level 1).

Iterative attacks take a -2 penalty on the attack roll.

Power Attack and Combat expertise provide double bonus in exchange for penalties since the max BAB went from 20 to 12. Other bonuses and penalties are currently unchanged.