- At present, the first level of a class with a good save progression gives +2 to that save. (Unless this has been errata'd or FAQ'd somewhere, ) If you have multiple classes with a good progression in the same save, the bonuses stack. If you took the first level of each of 20 classes with a good will save, for example, your base will save modifier would be +40 (though your base modifiers for the other saves might be severely stunted, as would most of your class features).
- Nobody likes taking the Great Fortitude, Lightning Reflexes, and Iron Will feats. People that do take them almost always do so to fulfill a prerequisite for something more interesting, commonly a prestige class.
- Iron Will, at least, has been established as not really being worth a feat. Spending 3,000 gp and some time in the prison known as the Otyugh Hole will give it to a character as a bonus feat. As Great Fortitude and Lightning Reflexes provide similar benefits, but for the other saves, they are, by extension, also not really worth a feat.
With those two points in mind, I submit the following house rule for the forum as a collective to tear apart.
- For each saving throw (fortitude, reflex, and will), your base saving throw bonus equals (2X + 3Y)/6, where X is the number of bad progression levels you have for that save, and Y is the number of good progression levels.
- If you have at least one good progression level for a save, you gain the associated feat as a bonus feat: a level with a good fortitude save gives you Great Fortitude, a level with a good reflex save gives you Lightning Reflexes, and a level with a good will save gives you Iron Will. You can gain more than one of these at the same level if your class has more than one good save; for example, a Monk 1 will have all three as bonus feats.
If you only ever take levels in one class, your base save bonus under this system is the same as it would be with fractional saves (from Unearthed Arcana).
If you take levels in several classes with the same good save, your bonus for that save will be lower (by 2 points per class after the first), but I'm not terribly worried about this because existing save DC's are calibrated for the single-class save progressions.
You will not be able to take the save-boosting feats a second time, but as that is considered a poor use of a feat I don't think losing the option will upset anyone too much - if anything, it removes a trap for new players. Some feats and prestige classes are easier to qualify for, because it is easier to pay their feat tax. Again, nobody likes feat taxes, so a reasonable proposal to alleviate them should be well-received.
The Great Fortitude, Lightning Reflexes, and Iron Will feats are unchanged; you can still take them if you don't have any good-progression levels for the relevant save. If you later gain a good-progression level for that save, you can (as part of leveling up) retrain your newly redundant feat into another feat whose prerequisites you met at the time you originally gained the redundant feat.
tl;dr: Good save progressions now give the initial +2 bonus in the form of a weak bonus feat, rather than directly. Numbers are mostly the same, but some side effects are nicer.