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If you bomb Iran's nuclear capacity and you don't capitulate the theocracy, you open yourself up to state-sponsored nuclear terrorism. Make no mistake, the Iranians will retaliate if attacked so long as there is continuity with respect to command and control. In the real world, the military answer brings with it the baggage of occupation and nation building. Our military is stretched as it is now - even if we were so inclined as to attack, logistically, we're not in a position to conduct such operations.
Also, Iran is overwhelmingly Shia where Afghanistan and Iraq are Sunni - so how you treat each nation and the progress each makes will be held up for comparison. This could also spell trouble as we could be seen as being more for one arm of Islam than the other.
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