Currently when you are a monster class you don't get anything from your other class right when you dont get a HD right? If this is not true then the rest of the post is moot.
If this is the case however then hear me out. Say you were a Stone giant//Wizard (cause you're weird) the Stone giant gets a 1 HD per level until level 3. So you would be a Stone giant 3// Wizard 3. This is all fine, but things get weird when you don't get a HD. At level 4 You would be a Stone Giant 4// Wizard 3 because there was no HD gain from that level. Now a fully level Stone Giant would be Stone Giant 18//Wizard 14. You have the experience of a level 18 character but one side is effectively 14. The savage progressions normally replace class levels. A stone giant has an 18 level progression because it is roughly as strong as an 18th level character. To put this into better perspective an 18th level Stone giant is as strong as an 18th level Fighter. But using gestalt rules you can be a Fighter 18//Wizard 18 and the Stone Giant is effectively Stone Giant 18// Wizard 14. Both characters have the same exact experience but the fighter has four more levels. To fix this disconnect I propose that the HD of creature not affect class abilities. As far as I can tell HD affects Bab, saves, skill points, and feats. Not class abilities. So a Stone Giant 18//Wizard 18 would have 14 HD, 4 feats, 14 levels worth of skills, and 14 levels worth of save progression, +10 Bab (Stone giant only have a 3/4 progression), 18 caster levels, 3 wizard bonus feats, and 9th level casting. I think this is a happy balance from what we first thought how it worked and how it currently works.
If this is already how this is supposed to work then I guess I am just confirming it cause I was confused.