Here's a small addendum to my previous list of lessons regarding easy debugability of microcontroller boards.
It's not a bad idea to pay a bit of extra attention to the connectors that will be used when developing and debugging software. It's likely these will see much more use than any other connector on the board, especially if the board is also meant for teaching or research like VESNA.
The first concern is that it should be hard to connect it in a wrong way. IDC and similar pin header connectors are popular for JTAG. Use a male part that has a shroud so that it's impossible to connect it when displaced by a pin or turned 180 degrees. That might sound obvious, but when you're debugging that tricky race condition and switching the debugger between three systems on your table late in the evening, the last thing you need is a burned out board because of a misplaced connector.
The other thing that is also worth considering is the life time of the connector itself. While the life time of the part on the board might not be problematic, the part that stays with the developer can be. For VESNA one of the most common reasons to make a trip to the soldering station is a torn wire in the connector for the serial debug console. We use something similar to the Berg connector and that one doesn't really take many connect-disconnect cycles before either wires get torn out or little springs break and the metal part falls out of the plastic housing. It's not always obvious that has happened and again it's a pain to realize after a long debugging session that the reason a board is talking garbage is not due to a bug you're trying to catch but rather due to a broken ground line in your debug console.