Doh, I thought I was the first one that thought of doing this.
Gestalt is one case where fractional BAB/saves can be sub-optimal. Esp since you can progress each side so that they cover the other side's weakness.
Consider PRCs like the prestige Paladin that improves spell casting every 2 levels. Basically, for the dead levels, if you plug in another class with full casting, you don't lose any caster levels at all. Eg
1) X / Cleric 1
2) X / PRC Paladin1
3) X / Cleric 2
4) Cleric 3 / PRC Paladin2
5) X / Cleric 4
6) X / PRC Paladin3
7) X / Cleric 5
8) Cleric 6 / PRC Paladin4
9) X / Cleric 7
You know and can cast spells exactly like a level 9 cleric.
Now, instead of the PRC Paladin that gains a spell level every 2 levels, consider the wizard that gains 1 BAB every 2 level, who uses a fighter level to shore up the dead BAB levels. It's not that much different.