Take a sorcerer paladin. Good spells, good saves, good base attack. Then you run into armor problems - either you wear armor and cripple your spells or don't wear any and then have AC problems. Also, feat availability becomes a problem as well since you don't have enough for combat feats and spell feats. Cleric rogues also suffer from armor restrictions (evasion, tumble) and multiple attribute dependency. Dex usually isn't a cleric's forte. Many gestalt class combos require trading off elements of one class to use parts of the other. That's especially true in play, because characters have a limited time to act. If the paladin sorcerer is swining his sword and smiting some guy, he's not casting spells. If he hangs back and fries the enemy, then he's not being much different from the Paladin 2/ Sorc X normal multiclass.
Something like a fighter barbarian doesn't gain much in versatility, but he ends up with a staggering melee specialization. Greater Rage + Greater Specialization = ouch. Everything in the popular Barbarian Fighter multiclass, but with more hurting! Taking rogue instead of either fighter or barbarian might lead to more potential raw damage, but it'll lack the stacked to hit bonuses and probably have trouble generating flanking for frequent sneak attacks. When using Barbarian abilities, the fighter abilities also come into play.
But yes, some combos are better than others.