The E46 manual are rare. I have only encountered SMGs with the E46 (and rarely 6sp). That reason i am lead to believe the 6sp was an option rather than standard but i guess both could have been made available from factory upon ordering at purchase.
As for the E92, if SMG was only released 2 months ago, that would made the first batch of E92 with standard manual.
I too have driven both SMG and 6sp E46 M3s and i prefer manual. In heavy traffic SMG but SMG is hard to drive/ park if you're not used to it.
I will not be able to afford either IS-F or M3 but if i can and will get one, i'll get manual, just want the feel of manual shifting the old fashion way. Speed isn't everything but with these cars you need to be with them in the mind, body and soul.