Hoping to clarify the fractionals a bit in case you're confused:
Fighters of course have 1/1 BAB. Clerics and rogues, etc, have 3/4, and wizards etc have 1/2. Going this route helps a bit if multiclassing is common in the game.
And then there's gestalt. Depending on one's interpretation, going fighter 1/wizard 19//sorc 20 would give a total of +20 BAB. The reasoning behind that is that since both sorc and wizard get 1 BAB every other level, staggering them would mean they got 1 BAB every level, thus 20 BAB. Going fractional fixes that problem because both sorc and wiz are 1/2, so the end result of the aforementioned character would be 10 and 1/2 BAB at 20th (since the fighter grants an extra 1/2 above sorc or wiz).
Saves could theoretically be exploited in a similar way, although I'm not sure of the exact setup right now. Still, saves are either 2 + 1/2xlevel or 1/3xlevel. Preventing them from going above a single-classed Good progression for base saves I suppose might be a way to prevent "abusive" save-stacking tricks so that they aren't trivializing saves, but it's not something I've heard of being used often.
Edit: Actually, that fighter/wiz//sorc one would work for saves too. The character would start with Will +2 on the sorc side and +0 on the fighter. Then at 2nd level the sorc side would get a +1 (ignoring the wizard's +2 start for the purposes of this demonstration). At 3rd level, the wizard side gets a +1 while the sorc side gets a +0, and so they alternate until the character has a base will save of 21 I think at 20th level. Going the fractional route would make both sides simply +1/2 after the +2 starting save for the class.
Shame they didn't put much into the gestalt rules to make sure that BAB or save tricks like avoid could be totally avoided, but considering it's a variant I suppose they really didn't playtest it much or go through their wording to make it absolutely clear what they wanted to convey, if of course they knew what they wanted to convey anyway.