Grifman said:1) The Ebonhawk falls to its apparent destruction then magically appears at the end to fly away our hero
They just don't build them like they used to. After the crash of the ship in to that rock, that should have been all she wrote for that thing. You don't just slam wedge yourself in to rock if you're hollow and metal and just fly away later.
2) There is an unresolved confrontation between GOTO and T3
You mean "remote"?
3) Mira appears magically, fights Hanharr, then magically disappears
What about Bao-Dur? He sends remote out to do the gravity wave bit, and then disappears.