I got my Indian and Iranian visas in Turkey without going through an agency. Was stuffed around by the Iranian consulate in Istanbul, but eventually managed to get it in Erzurum. I had also tried to get my Pakistan visa in Istanbul, but was told to get it in Tehran. That ended up being only a 4 day wait.
I don't know what the situation is now, but it shouldn't be too different. I suppose if you are in a hurry, or have a definite timetable, getting your visas at home would be the go.
Kenny
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