Hey Marcus... I'm Dan of Rheingold Heavy, the guy who wrote the review. I just wanted to thank you for taking the time to come out here and engage with us.
I like the idea of an online-for-the-masses EDA tool, but I've actually done layout on a laptop in my father's house with no internet connection. There's no way I could cobble together a schematic without being able to look at datasheets, but the PCB layout and routing doesn't necessarily need to be always-connected.
I tried using Upverter either earlier this year or late last year, can't remember when, and I just remember that I struggled with the interface. That's not a smack on Upverter though, just an incompatibility between the tool and the idiot trying to use it :)
Chris Gammell of The Amp Hour is also getting http://kicad.info off the ground and there are some really great people providing advice in there.
I've gotten burned too many times using the built-in libraries (hidden pins in EESchema not being connected to PWR/GND / incorrect pin spacing in CvPCB) so I throw those together by hand now. In EESchema I would have done it anyway, just to get the pins arranged in a way that makes my drawing look purrrrty, but the drawing/verifying of footprints does get tedious.
My understanding is that some features were removed (or significantly modified) in subsequent releases of KiCad post the version I'm using (BZR 4022), specifically the BOM export, so I haven't bothered installing another version yet. I have a series of designs about to go into production so I'm leery to change up before those boards get committed for assembly.
Back when I decided to pick an economical design tool, I had a four layer board to design and the price was right with KiCad, so I never got into using EAGLE. The clearance issue is one that I do have to wrap my brain around each time I do it, just like pin spacing on custom footprints. I put that down to my own personal issues with keeping three digit numbers straight in my head though, rather than any particular problem with KiCad in general. That's why I consider doing the Gerber visual diff so vital, because it's very easy to tell when you've screwed up the solder vs. paste clearance.