Yeah, I was thinking about that. These rules would probably be better with new gestalt classes, but I'm too lazy to do that right now.
Here's another thought. How exactly should I handle the change from gestalt to normal at 4th level? I can see two ways of doing it:
1) Use normal gestalt rules for each stat (BAB, HD, saves, etc) on each side, but one side never gets better after 3rd level, so eventually, you'll likely be using your normal class for all of your stats. For example: a wizard 9//orc paragon 3 would have a BAB of 4, base Fort and Ref of 3, and base Will of 6. All of these stats are greater or equal to the orc paragon stats, so by this point, the paragon will have little or no effect on these stats.
2) Use the normal gestalt rules for each stat for the first three levels, and stack on top of that from 4th level and beyond. Don't double-count the initial +2 save bonus for any class. This makes the paragon class more important for determining these stats throughout the character's career.
Just to illustrate this, let's look at a wizard 5//orc paragon 3 with both scenarios:
1) Wizard 5 provides BAB +2, Fort + 1, Ref + 1, Will + 4. Orc paragon 3 provides BAB +3, Fort + 3, Ref + 1, Will + 1. So, this 5th level character would have BAB +3, Fort +3, Ref +1, Will +4. This character's BAB won't increase to +4 until level 8 and his Fort won't increase to +4 until level 12 (assuming he stays straight wizard).
2) First we figure out the gestalt rules to figure the first 3 levels. Wizard 3 provides BAB +1, Fort + 1, Ref + 1, Will + 3. Orc paragon 3 provides BAB +3, Fort + 3, Ref + 1, Will + 1. So, this 5th level character would have BAB +3, Fort +3, Ref +1, Will +3. So the 3rd level stats would be BAB +3, Fort +3, Ref +1, WIll +3. Next, we add two more wizard levels on top of that*. Two wizard levels would add BAB + 1, Fort + 0, Ref + 0, Will + 1, for a total of BAB +4, Fort +3, Ref +1, Will +4. This route seems far more complicated to me, for relatively little gain. It will, however, allow for a smoother advancement after 3rd level.
* I guess the best way to calculate these bonuses would be to take the class level and subtract any taken during the first three levels. So the example above, 5 - 3 = 2, so we look at the stats of a 2nd level wizard to determine what's added on top of the 3rd level gestalt stats. Because we already counted the +2 Will bonus a wizard gets at 1st level, we have to subtract 2 from the Will value listed on the table for a level 2 wizard. So, at 10th level, we add the stats of a 7th level wizard (10 - 3 = 7) to the level 3 gestalt base, again, subtracting 2 from a level 7 wizard's Will. So this would add BAB + 3, Fort + 2, Ref + 2, Will + 3 (not 5) to the gestalt base.
Multiclassing isn't so bad. Again, what we're trying to avoid is counting the +2 bonus to a save for any class more than once while allowing for continued advancement. So if after 3 Wizard//Orc Paragon levels we take 2 levels of fighter, we add BAB +2, Fort + 3, Ref + 0, Will +0. We add the full Fort bonus of +3 because this character does not yet have any fighter levels.
Had the character been something weird like Wizard 1/Cleric 1/Fighter 1//Orc Paragon 3, any wizard, cleric, or fighter levels added on afterward would not gain the +2 Fort and/or Will granted by the class at 1st level. Adding something like rogue, however, would grant the full +2 Ref from 1st level because there are no rogue levels in the first three gestalt levels.
Confused yet?
Wow this post got long! So, if you're still with me, which route do you prefer? The simple route which has the potential for slow advancement form levels 4 - 9, or the complicated gestalt stacking advancement?