On the door : They put the wiring for the power/reset/hdd on the actual door of the mirage (the eclipse has it on the frame), so when removing the door to add a fan for example, you have to route the cables through the front of the case. Pain in the ass.
On the exernal connectors : The Mirage has 2 usb, audio and a firewire connector on the right side. The firewire is crap though as it has no mobo connector. It's an external job, so you either route it out the back of a pci slot and connect it externally or find an adaptor to connect it to your motherboard.
On the pci slot on the front : gone from the Mirage. pants. it was useful for say a fan controller for a tuniq tower.
On the quality of the door : crap...it marks easily, and even though it has vents, airflow is slightly impeded over the Eclipse (maybe 1 or 2 degrees at most for system temps).
Other things : the wireguide inside the mirage is black to match the rest of the case. the eclipse (except on recent models) is a different colour.
Also, for some reason my HD lead is permanently on.
The sidepanel you mentioned is the optional thermally advanced panel and useful for cooling the hot spot over your gpu. It fits on the Eclipse and Mirage though of the 3 or 4 I have seen sometimes the panel gaps are poor and you don't get a great fit. The panel actually can rattle a bit when you touch it. Luckily I got a good 'un.