From my wishlist:
Wake on Lan - yep, I know that Helios64 supports WOL, but practically it is still not working
a properly wired 2.5 GB connector - yep, I know, but it is frustrating anyways, especially due to the warranty handling of kobol (send it back on your risk, wait 2 month, send a replacement back, wait another 2 month, hope it works)
standard SATA connectors - my ZFS fails rather often due to checksum errors, this seems to be related to bad cables. With the shipped non-standard cables, this is however hard to solve. If the enclose / board had standard connectors, I