I have several assocaite-omatic stores that I was able to set up within minutes. I never had any problem with ioncube. I think if people do experience difficulty with that, it's a server issue, since some hosts don't support IC.
At any rate, I was able to set up a store pretty quickly, and then spent several days working on colours, a header graphic, etc. I know you can get premade templates for it, but I was happy enough with the way I did it. I have some PHP experience, so I could always go into the template files if I wanted to do some serious tweaks. I think most people would rather go the easy route like I did.
I have made sales on my sites, so it's working fine for me. I guess I could promote my stores a little more and drive more traffic, but considering the amount of effort I've put in so far, I have to say that I'm quite pleased.