Removable tray (or lack thereof) isn't really what would make the reversible method more difficult to upgrade. The difficult part would be that when a new connector standard comes out, I'd have to source new panel mount extensions and modify my connector panel to accommodate. Using the rear bucket cutouts as-is was pretty much what I would do if I go the reversible route. I gave it more in-depth thought, and I decided HDMI, ethernet, and a few USB is all I'll probably need. My ITX board has other connectors for SPDIF audio and PS/2, but I won't be using them and can't imagine ever needing to. How often do new connector standards come out? Maybe not for another decade? So maybe making it reversible doesn't really mean upgrades would be any more difficult or expensive if connectors don't change. It would be messier on the inside with all the short extension cables, but cleaner on the outside.
Here are Photoshop mockups of my 2 ideas (it's actually the back of a Classic II, but close enough).
Easier future upgrades - making it a fully standard Mini ITX case that fits a standard I/O shield with all ports available, minimal internal wiring so cleaner on the inside, but an ugly VGA loopback cable on the outside.
Reversible - Should be possible to get all ports I'd ever need installed into the existing bucket holes. Ports won't be mounted to the bucket itself, but a plastic panel bracket I will construct. It will have USB 2.0 in the ADB and printer port holes, HDMI in the DB19, 2x USB 3.0 in the DB25, and I may go ahead and wire a headphone jack to the motherboard's front audio connector.
I actually think I can make it look fairly close to my mockups and I don't think either looks too much like a hack-job. I have seen someone widen the 3.5 floppy slot for a slot-load DVD drive and that did seem like a pretty cool idea, but I actually have no use for an optical drive at all on this machine. I'll probably just turn the 3.5" floppy slot into a stealthy 4-port front USB since it's just tall enough for a USB plug to fit into.