I'm not ignorant of the internal killings and the unrest stirred up by the extemists in these countries, but the fact is that these governments are moderate (as are the majority of their muslim population) and are working with the international community and particlulary the west, to strengthen their response to these internal extremists and to institute political and judicial reforms, albeit not as quickly or as succesfully as we would like.
If we want them to continue, its in our interest not to inflame their more moderate muslim populations with policies like attacking a sovereign muslim country that did not pose a direct threat to us and where our actions killed thousands of innocent muslim civilians, locking up (some for years at a time now with no outside contact) and torturing "suspected" muslim terrorists with no opportunity to prove their innocence, making references to islamofacists, etc.
Edit:
I agree with you on Iraq/Iran connection . The result of our invasion was to create a scenario where SCIRI and Dawa (the two shia sectarian political groups with connections to Iran) would be in control of the government and would strengthen ties to Iran.
Iran, Iraq to strengthen security, intelligence ties
I think it was Howard Dean who predicted this before the war
