I have been play testing Mystic Theurge builds for about a year. There are in essence two decent/good builds.
1) focus on cleric spells
2) focus on wizard spells
The best class build I have found is:
Mystic Theurges always fight defensively and only cast attack spells that do not require attack rolls, such as (acid) burning hands / (acid) fireball, (acid) flaming sphere, magic missile, etc.
1 level dip spire defender (magus): +int to concentration (this is why magus: if you think your GM will not target you - the caster - then don't bother with magus) + dodge feat (+1 AC) + combat expertise (+1 AC +1 additional AC/4 BAB when fighting defensively) + exotic weapon focus (nine section whip: +1 AC when fighting defensively) + (always chose feather fall as one of the magus' spells)
1 level dip into crossblooded sorcerer (orc / dragon (acid)) +2 damage per dice rolled when casting acid spells
1 level dip into cleric (trickery / travel) (+10 movement)
1 level dip into admixture wizard (able to change normal spells into acid spells, +1 damage when casting acid spells)
Mystic Theurge 1-10
Then more of either wizard or cleric until Level 20.
I know the build above looks dumb, but in my current L11 group, my MT has the 2nd highest AC (before combat buffs) and does the most DPR... by a lot.
*** I am currently exploring the ?maybe? brokenness of Aasimar: Oracle 3, Cleric 1, Inquisitor 1, Hellknight Enforcer 1 (Warrior Priest feat: cleric, oracle, inquisitor), Evangelist 10 (Hellknight Enforcer), then more Oracle build.