The mystic theurge is hardly a bad class. Allow me to provide a brief history lesson. When the 3.5 edition was in the works and this was one of the first previews we had of the system, it was without the proper context of the 3.5 rules as a whole. Players and DMs alike looked at this class and said to themselves that it was the most broken piece of crap they had ever seen. The first reason was buff spells like bull's strength and fox's cunning. These spells had 1 hour/level durations and could be metamagically enhanced. The mystic theurge, with his abundance of spells, could theoretically easily afford to keep them handy at all times. The second reason was haste, the action booster. More spells + more spells per round = better character. Finally, there was simply the fact that no one had ever played one besides playtesters.
When the mystic theurge showed up on the scene, there were a lot of changes to the rules that came along with it, things that people did not necessarily anticipate. Of major note was the change to haste, which seriously mitigated any previous "OMGSFB!" reactions. Additionally, other buff spells like magic vestment, greater magic weapon, bull's strength, and the like were "nerfed," either by reducing their durations or their effect. After several years worth of experience, we have seen several variations on the "prestige class as multiclass" idea and honestly, it hasn't caused huge problems for people in most cases. One major deterrent to actually playing a mystic theurge is the process of becoming a mystic theurge, a process which involves six levels in two classes that must be spread evenly between each other. Compare a 3rd-level cleric/3rd-level wizard to almost any other 6th level character, multiclass characters usually included, and the mystic theurge wannabe is quite limited in power.
At any rate, the mystic theurge is not broken. Ultimately, the class is sub-par at spellcasting and simply trades potential for stamina. Your DM may be concerned about the mystic theurge if he is running 3e, but if he is running 3.5, he was probably caught up in the initial fear of the class and never moved beyond it, or he has limited experience DMing (either in general or just with this rules set) and doesn't want to introduce such a wild card effect into his game. Or he may have another reason, but I think we are past the days when everyone cries foul at the mystic theurge. I think popular conception now holds that it is a pretty balanced class that has become the paradigm for multiclass caster prestige classes.