The mystic theurge is one of many core prestige classes regarded as a poor choice. By the time you enter it, you have sacrificed critical spell levels. Then, you proceed to lose all class feature progression. Trading class features for spellcasting seems reasonable, but shouldn't that spellcasting keep up? Many have tackled this issue. My own colleagues at Multiclass Productions have their sacred thaumaturge wizard archetype.

A random post of mine in a thread on the Paizo forums suggesting that the mystic theurge just be turned into a 20-level base class with no added bells or whistles or complications met with positivity, so here's a formalization of the concept.

Alignment: any, but chaotic is discouraged.

Hit Die: d6.

Class Skills

The mystic theurge's class skills are Appraise (Int), Craft (Int), Fly (Dex), Heal (Wis), Knowledge (all) (Int), Linguistics (Int), Profession (Wis), Sense Motive (Wis), and Spellcraft (int).

Skill Ranks per Level: 2 + Int modifier.

Table 1-1: Mystic Theurge

Level BAB Fort Ref Will Special Spell Progression
1st +0 +0 +0 +2 +1 arcane, +1 divine
2nd +1 +0 +0 +3 +1 arcane, +1 divine
3rd +1 +1 +1 +3 +1 arcane, +1 divine
4th +2 +1 +1 +4 +1 arcane, +1 divine
5th +2 +1 +1 +4 Combined spells (1st) +1 arcane, +1 divine
6th +3 +2 +2 +5 +1 arcane, +1 divine
7th +3 +2 +2 +5 Combined spells (2nd) +1 arcane, +1 divine
8th +4 +2 +2 +6 +1 arcane, +1 divine
9th +4 +3 +3 +6 Combined spells (3rd) +1 arcane, +1 divine
10th +5 +3 +3 +7 Spell synthesis (1/day) +1 arcane, +1 divine
11th +5 +3 +3 +7 Combined spells (4th) +1 arcane, +1 divine
12th +6 +4 +4 +8 +1 arcane, +1 divine
13th +6 +4 +4 +8 Combined spells (5th) +1 arcane, +1 divine
14th +7 +4 +4 +9 +1 arcane, +1 divine
15th +7 +5 +5 +9 Combined spells (6th), spell synthesis (2/day) +1 arcane, +1 divine
16th +8 +5 +5 +10 +1 arcane, +1 divine
17th +8 +5 +5 +10 Combined spells (7th) +1 arcane, +1 divine
18th +9 +6 +6 +11 +1 arcane, +1 divine
19th +9 +6 +6 +11 Combined spells (8th) +1 arcane, +1 divine
20th +10 +6 +6 +12 Spell synthesis (3/day) +1 arcane, +1 divine

Class Features

The following are the class features of the mystic theurge.

Weapon and Armor Proficiency: Mystic theurges are proficient with the club, dagger, heavy crossbow, light crossbow, and quarterstaff. Mystic theurges are not proficient with any type of armor or shield.

Spells: At 1st level, the mystic theurge selects one divine spellcasting class and one arcane spellcasting class. The mystic theurge gains the spellcasting methods of those classes. The mystic theurge's spellcasting progresses as though he had levels in each of those classes equal to his mystic theurge level. For the purposes of determining spells per day and spell DCs for each of his spellcasting methods, the mystic theurge uses the ability score that he would use if he were the class whence that method derived. (For example, if the mystic theurge selects the sorcerer's casting progression, he uses his Charisma score and modifier for his arcane spellcasting.) If the mystic theurge's spellcasting methods require tools (such as spellbooks or divine focuses), the mystic theurge is capable of using these tools.

Armored Casting: The mystic theurge ignores arcane spell failure while wearing light armor if his arcane spellcasting progression is taken from a class that ignores arcane spell failure, such as the bard or magus. This does not apply to arcane spells received from other classes.

Combined Spells (Su): A mystic theurge can prepare and cast spells from one of his spellcasting methods using the available slots from any of his other spellcasting methods. Spells prepared or cast in this way take up a slot one level higher than they originally occupied. This ability cannot be used to cast a spell at a lower level if that spell exists on both spell lists. At 5th level, a mystic theurge can prepare 1st-level spells from one of his spellcasting classes using the 2nd-level slots of the other spellcasting class. Every two levels thereafter, the level of spells that can be cast in this way increases by one, to a maximum of 8th-level spells at 19th level (these spells would take up 9th-level spell slots).

The components of these spells do not change, but they otherwise follow the rules for the spellcasting method used to cast the spell. If one of the mystic theurge's spellcasting methods is spontaneous and the other prepared, he can only cast a spell from his other method using his spontaneous casting slots if he prepared that spell that day, though this functions even if the spell has already been cast. For example, a mystic theurge with cleric and sorcerer spellcasting can use this ability to spontaneously cast a bless spell using a 2nd-level sorcerer spell slot, if the character had a prepared bless spell using a 1st-level cleric spell slot, even if that spell had already been cast that day.

Spell Synthesis (Su): At 10th level, a mystic theurge can cast two spells, one from each of his spellcasting classes, using one action. Both of the spells must have the same casting time. The mystic theurge can make any decisions concerning the spells independently. Any target affected by both spells takes a -2 penalty on saves made against each spell. The mystic theurge receives a +2 bonus on caster level checks made to overcome spell resistance with both spells if they share a target. The mystic theurge may use this ability once per day at 10th level and one additional time per every five levels thereafter, to a maximum of 3 times per day at 20th level.