Here is another question to consider: why would dual caster classes be treated differently from other prestige classes involving a combination of caster class and non-caster class?
Arcane Trickster gets full caster level increase and full sneak attack progression. Eldritch Knight gets full caster level increase, and BAB progresses the same way a fighter's would at the same level. In neither case do we progress the feature of one class on odd levels and one class on even levels. Instead, the basic feature of each class progresses each level.
I'm not familiar enough with PNP to know why such distinctions were made in the first place. Perhaps the feeling was that an epic dual caster would be too powerful. On the other hand, it seems clear that there is little point in an epic prestige caster class that progresses exactly like alternating the two base classes would progress, but without any of the other class features. Using the Mystic Theurge as an example, after the first 10 levels, if divine casting improves only on odd levels and arcane only on even levels, then the situation is exactly the same as just alternating the two base classes, except that the character loses turn undead progression and familiar progression, and probably takes a little hit on BAB. Who would do that?
As a consequence, it probably isn't worth coding epic progression for Eldritch Theurge and Eldritch Disciple if both invoking and casting don't progress each level. In terms of character optimization, a player's best strategy would be to choose one base class or the other after the ten levels of the prestige class and be a full invoker or full caster, with the other style of magic as a secondary supplement. Others might disagree, but that is my feeling on the issue.
