When gaining levels, with saving throws in mind, it can be a very munchkin-like tactic to multiclass to get the additional +2 on the main saving throw. I propose a more balanced, though more complex, means of determining it. As you all know a main saving throw increases every multiple of 2 levels, while secondary saving throws increase every multiple of 3 levels. I propose to maintain this, but to do so in that you increase it, not by the class level, but by the character level.
For example, Oleff starts out as a Ftr1, thus having saving throws such as +2 Fort, +0 Ref, +0 Will. After battling kobold after kobold, he gains the so wonderful 1,000 XP he deserves and get to level up. At this point, Oleff has ponder the more rogueish art of... well, rogues. So, for level 2, he decides to become a Ftr1/Rog1. Normally, he would gain a +2 to Reflex save, greatly boosting that throw, but I think that since he is originally a fighter, he wouldn't be that good as if he had originally studied to be a rogue. So instead, under my varient rules, his main saving throw would increase, since its level 2 (a multiple of 2, duh), by +1. Thus his scores would be +2 Fort, +1 Ref, +0 Will. After picking locks and stabbing goblins in the back from shadows, Oleff gains a well deserved 2,000 more XP, bringing him to 3,000 and enough to level up to 3. At this point, he misses the hack and slash methods of a fighter, and decides to become a Ftr2/Rog1. At this point, its level 3, a multiple of 3 and when the secondary saving throw(s) are increased. Normally, his Fort would increase from +2 to +3, but under this method, his Ref and Will would increase, thus making his saving throws +2 Fort, +2 Ref, +1 Will.
This method DOES give players a chance to plan which saving throws are strong, but I feel this can all so be used to make you character more to your desire by giving the player a chance to control his/her PC's strength/weaknesses. If you want a character who could resist any will save without even having to look at the dice, but will drop at even the mention of poison and fort saves, so be it.