Multiclassing in general is pretty wonky. Spellcaster + non-spellcaster is kinda broken, and not in a good way. And so on. But you mightn't be wanting to hear about all that. . .
Spellcaster + Spellcaster is even worse.
I saw an elegant solution on the Paizo boards though, as a replacement for things like the Mystic Theurge. One feat that functionally replaces all of the Ascetic/Devoted/Stalker feats from
Complete Adventurer and
Complete Scoundrel.
Pick two base classes you have levels in. (Or two base classes whose levels are within 1 of each other, if you want to be strict.) Your levels in these two classes stack for the purpose of determining level based effects (such as class level prerequisite, caster level or class ability DC), and one half of your level in each class stacks with the other class for determining class features, including special abilities and spells per day.
In other words, a Cleric 10/Wizard 10 with this feat would have a caster level in both classes of 20, would cast spells in both classes as a 15th level caster, turn undead as a 15th level Cleric and have the familiar of a 15th level Wizard.
A Fighter 10/Rogue 10 would have 8d6 sneak attack, all the other nifty tricks of a Rogue 15, eight bonus Fighter feats, and would count as Fighter 20 for the prerequisites of everything in the Weapon Specialization chain.
Mileage may vary on allowing this feat to be taken multiple times for different classes, or for allowing characters to use this feat with classes more than 1 level apart. One variant I saw was that for every level of difference, subtract 1 from the effective level of the lower class, which I thought was particularly elegant.
Of course, the other thing to consider is that it did not, under any circumstances, apply to Prestige Classes.