I have both but find myself using my old tried and true Aperture 3 more than my new C1. Hard to teach an ole dog new tricks I guess. I find those files I do process in C1 I still move to aperture for a final touch up and filing.
I lost access to a whole file of aperture saved master files stored on a external hard drive by downloading them into C1 when I was first playing with the program. Seems it wrote code to these masters which Aperture could no longer access. Needless to say I was not a happy camper and this never happened when my DXO PP software was used the same way. To make a long story short after hours of hopeful work I still permanently lost Aperture access to 126 images. I never took a file from my aperture masters and downloaded them into C1 again...... the old "burn me once" scenario. I heard this has been fixed but I just can't get myself to do that again to find out for sure.
I really like what C1 does for my a77 and NEX 7 files but I am very selective on what I bring into C1 making sure I have files saved in other locations first.
I will be the first to admit I am very new with C1 and guess I should of signed up for a webinar .. but even after months of owning it I am still uncomfortable with the catalog/session aspect as well as some of the functions like overlays.So I just export it to CS6 if I need overlays or other functions that confuse me on C1.
I currently use CS6, DXO8, C1Pro7, and Aperture 3 as my basic PP softwares with Photomatix, DXO viewpoint, Topaz suite, Portrait professional, and a couple other plugins for my photos. Of them all C1 is the most confusing for me at this time.