All other things being equal, my money's on the theocracy.
Assuming the gods stay out of it, my money's still on the theocracy.
Here's my reasoning:
1. Would you rather adventure in a party without a wizard or a party without a cleric?
2. The primary ability of the mageocracy is intelligence so they'll be able to come up with some creative plans and good analysis of situations. However, the primary ability of clerics is wisdom which means that they will be able to pick the most advantageous alternative available to them. They will be more likely than the wizards to see through their opponent's deceptions as well.
3. Clerics and paladins typically make more dynamic leaders than wizards or fighters. Charisma is a dump score for wizards and fighters. Clerics and paladins tend to have above average charisma. This would probably translate into higher morale and better discipline (since paladins would provide a good example to their troops and would also be more inspiring when convincing them to put their lives on the line) in their armies.
4. Did I mention that diplomacy is a class skill for clerics and paladins? This is likely to result in more harmonious and productive discussions among the leadership and will probably make outside forces more likely to support the theocracy. Granted, the wizards have charms and dominates but most rulers in a fantasy realm are well protected against such effects. (And some clerical domains grant similar spells).
5. The best clerical summoning spells are much easier and less time consuming to cast (compare the planar ally spells to planar binding spells--no preparation, lengthy rituals, risky circle inscribing, additional spells (dimensional anchor) or anything else is required for the planar ally series. Payment is required by both but beings summoned by planar binding are more likely to ask for payment in advance).
6. Clerical spells are really quite effective in the direct damage department (burning hands and produce flame (fire domain), sound burst, blade barrier, briar web, spiritual weapon, storm of vengeance, searing light, and flame strike, Holy Word, firestorm, symbol, control weather) although they're admittedly inferior to wizard spells. On the other hand, clerics have better (IMHO) buffing spells (bless, prayer, heroes' feast, shield of law, spell immunity), undisputed mastery of healing spells, and a better spread of divination spells (augury and divination--plus access to detect thoughts through the knowledge domain).
7. Harm
(Mass heal isn't half bad either).