1) The GUI is slow.
2) XML Configuration files are too fragile (that is, if there is an element in the config file that doesn’t match to the package, it blows up)
3) The GUI is too blinky, especially when you click run. [UPDATE: If you change the solution properties to *not* compile every project, the blink-i-ness goes away, but you will have to remember to manually build as appropriate.]
4) The GUI is slow.