I don't understand why people have problems with a 'non Star Wars' plot. It's a big galaxy with a long history, and chances are it isn't all sunshine and dasies. Taking a look at this darker side can't hurt.
Architect, are those definately the triggers for the NPC endings? I'm pretty sure there was infuence involved. I don't have the PC version, so I can't check, but if it is influence related, some of the lines (eg. Atton's 'I wanted to protect her...[snip!]...you showed up, playing hero.' line, which doesn't work logically unless the Exile has more influence over Michal) make more sense if the confrontation was based partially on influence, as DaveK said.
Does anyone know the intended triggers for the cutscenes (i.e. were there any partial placements found), or were none placed at all?