truth is they are basically the same thing, all current Marantz models are essentially rebadged Denons. Marantz and Denon are both owned by the same company (D&M Holdings)... there used to be more product differentiation but for the past few years the Marantz models have just been re-skinned Denons, presumably to save cost on the supply side. Marantz still customizes a bit (slightly different back panel input/output options, possibly some different component stuff on the analog side) but it's essentially the same thing. They even have the exact same GUI interface.
The 3312ci does have a PHONO input as well (you can check this yourself pretty easily by going to the product page and simply looking at the photo of the back panel). The SR6006 has 7.1ch analog multich inputs and dedicated FRONTB speaker posts, whereas the 3312ci doesn't have a "FrontB" post but it does have speaker posts for DSX speakers (F.Height + F.Wide). They both have the same featureset otherwise (MultEQ XT + Dyn EQ/VOl + DSX) although the 3312ci is spec'd as having more powerful amps.
Compare the photos of the back panel and note the striking similarity in the layout -- note the IDENTICAL location of speaker posts, HDMI inputs, component video inputs, digital audio inputs, ethernet port, RS-232 port, trigger outputs, pre-outs, etc.