Note the key wording in the Gestalt rules: "if the two classes you choose have aspects that overlap (such as Hit Dice, attack progression, saves, and class features common to more than one class), you choose the better aspect." When leveling a gestalt character, you cannot "double dip" the same class; you only get the better features of the two, not both.
Generally, you shouldn't switch from a being a standard character to a gestalt character (except at 1st-2nd character level, perhaps) or "tack on" gestalt levels (such as your fighter 4//wizard 2 example); tracking two sets of experience points/levels gets to be a real pain. If you want to give them a boon of an extra level (so they immediately become a fighter 4/wizard 2) for a specific reason, that would probably work better.
By gestalt rules, what you are proposing is to make a fighter 4 into a fighter 4//fighter 2/wizard 2 (4 total gestalt levels, fighter 4 on one side and fighter 2/wizard 2 on the other); you have fighter levels on both sides (which provide no benefits above a single-classed fighter for the first two levels). From this point forward, the character is a normal gestalt character (including all of the benefits and limitations), with a couple of "dead levels" on one side; the character will need to "spend" another level "rebuilding" into a "true" gestalt character; or the advancement on one side (the wizard levels) will need to be tracked separately (as with 1st/2nd AD&D multiclassing).
Because (again, by gestalt rules) the character gains no benefit for the fighter levels on the fighter 2/wizard 2 side, it may be easier just to give them a bonus level in their new class to speed their transition to a prestige class. Note that gestalt characters are more restricted in their choice of prestige classes and gain fewer benefits from many of them.
Gestalt characters are effectively around +1/+2 APL/CR, not +50% APL/CR. See the gestalt rules: "If you want to keep level advancement at the standard average of thirteen encounters per level, reduce the Challenge Ratings of all the monsters and NPCs in your campaign by 1 (or by 2 if they rely on failed PC saving throws to pose a challenge)." Even with the added abilities and toughness, the characters still only get one set of actions (plus pets/summoned creatures/cohorts as normal).
Hmm, if you want more versatility within one character, you could also expand Gestalt to combining three classes instead of two. It increases the power level, but likely less than normal Gestalt in comparison to no Gestalt.