@denniss, Are you using the current 1.2.0 (or whatever)? I was on 1.0 and started this project almost right after they came out of RC status. I wouldn't have jumped on something that new usually, but the configurable product options were (are) fantastic and necessary for that project. The biggest complaints and concerns with that 1.0 release weren't stability, it was all about speed because of the backend bloat. Granted, at the time almost all the installations talked about on the forums were in shared server environments. I'm sure that speed was one of the top things that the team tackled with their 1.1 and 1.2 releases. I haven't kept an up to date version on my staging server, so I can't say how much speedier it is now compared to last June, but I'd expect it to be a lot snappier.
I agree in theory on the segmentation of the markup and CSS, but I like systems (like wordpress, for popular example) where there is a simple themes folder containing function and design files. Again, I don't have a current version that I'm keeping up with, so the massive folder structure could have been paired down a bit. The version I was using didn't have the ability to assign product or category specific themes, that sounds really cool. That's one thing that I'm really starting to like about Joomla.
As far as other things than speed and buried files, the only thing I can think of is customizing the code base, which shouldn't be an issue on most stores that it is used for. We were taking the customizable products and upgrading the capability past what was available at the time (the budget didn't allow for just writing a whole lot from scratch). So at least with what we were doing, making custom modules was a lot harder and time consuming than for other systems (OsCom comes to mind). But overall, anyone that is going to need more functionality than what is built-in will likely have a custom storefront or something, so it's not a real big issue. And I'm sure that as the backend has been simplified and restructured, the process of writing modules has become easier as well.
But overall, please don't take my criticisms to mean that I don't like Magento. I'm just apprehensive about using it in production environments due to the massive mess that I had last summer with it (long, stressful story). I really think that anyone interested in developing E-com systems should check it out and start learning how it works, as I think it's possible to really take off as the premier open source E-com system.
