Ya, your fella needs to back and reread those small set of guidelines to Gestalt play. Firstly as to Bonus feats, there are two kinds of Bonus Feats you see. Character and Class, if you don't understand the difference you have 0 business playing Gestalt.
Your Character Level or Hit Dice (in the case of Monsters) determine Character bonus feats and stat increases. Character level also determines your Max Skill Rank.
Now things do get odd when it comes to Class Abilities
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A gestalt character gains the class features of both classes. A 1st-level gestalt rogue/cleric, for example, gets sneak attack +1d6, trapfinding, 1st-level cleric spells, and the ability to turn or rebuke undead. Class- and ability-based restrictions (such as arcane spell failure chance and a druid’s prohibition on wearing metal armor) apply normally to a gestalt character, no matter what the other class is.
A Wizard Sorcerer would get the spell casting of both classes.
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A gestalt character follows a similar procedure when he attains 2nd and subsequent levels. Each time he gains a new level, he chooses two classes, takes the best aspects of each, and applies them to his characteristics. A few caveats apply, however.
Keep in mind that Gestalt rules in total run about a page and a half minus class example combos. They really are less rules then guidelines and up to how a GM wants to implement them.
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Class features that two classes share (such as uncanny dodge) accrue at the rate of the faster class.
This one most people miss, especially with things like Uncanny Dodge. Mainly this guideline is aimed at stacking abilities off each other way sooner then they should. Uncanny Dodge stacking to Improved Uncanny Dodge. This may be where your buddy got the wrong idea about stacking Spell Caster classes. Yes, spell casting has the same name but they really aren't the same class features. I can't think of class that is identical spell casting, aside variants of a class, which aren't legal of multi-classing normally and aren't really legal for gestalt.
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Gestalt characters with more than one spellcasting class keep track of their spells per day separately.
This one take the piss out of the guy saying that you'd only get the spell casting off One of your two gestalt classes.
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A gestalt character can’t combine two prestige classes at any level, although it’s okay to combine a prestige class and a regular class.
One Prestige class at a time! Gestalt can already get crazy when you multi-class inside it but PrCs make it even nuttier to track. When it comes to prestige class that grant +1 Caster Level, these should flow established multi-classing guidelines. Each time you gain a "+1 Caster Level" you have to pick which qualifying class it applies to.
Now this is why Gestalt is more guidelines then rules. The rules don't explicitly prohibit you from taking a Prestige class with +1 Caster Level and a Level in the Spellcasters base class. However this goes partly in the face of "Two Classes sharing a Class Feature" guideline, also any GM or Player worth the bother can see very broken (even for gestalt) allowing that would be. Functionally it could allow Epic spell casting well before Epic. Like 6 levels too early.
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Prestige classes that are essentially class combinations-such as the arcane trickster, mystic theurge, and eldritch knight-should be prohibited if you’re using gestalt classes, because they unduly complicate the game balance of what’s already a high-powered variant. Because it’s possible for gestalt characters to qualify for prestige classes earlier than normal, the game master is entirely justified in toughening the prerequisites of a prestige class so it’s available only after 5th level, even for gestalt characters.
This one a GMs gotta really watch. A great many PrCs out there are at base combo classes. Although in most cases these PrCs look far less attractive next to just staying in your Base class.
Personally IMO the bigger issue over all with Gestalt play are the Savings throws with Multi-classing. The "normal" method breaks very fast. My personal house rule to the house rule is to "stack" levels of Save types. I also "stack" BABs.
Savings throws are Good or Bad. If you get a +1 Good save you increase the "level" of your Good Save progression.
Example (// is Gestalt break): Wizard 15 / Archmage 5 / / Fighter 10 / Barbarian 5 / Ranger 5 /
For Fortitude you'd normally add both the Fighter Barbarian and Ranger values together for +15. In my system you'd have gotten to Fort Good 20, for +12.
The more PrC/Class you stack on the worse the saves start scaling.