I remember way back when, that they said part of the original idea was how the Republic as seen in the EU before Palpatine was actually a mix of early Republic ideas and the Sith Imperial elements. So the suggestion was at some point after the Republic/Sith war as shown in the trailers for TOR, there would be a point of combining the two together to create what becomes the Republic as seen millennia down the road. Maybe that's what the whole Zakuul thing is meant to be, the lean towards that blending. Plus it's throwing out some reason for what the Emperor was doing since he wasn't really running his Sith Empire.
But yes, the ad-libbing feel is still there even with that sort of vague hand-wavey connections.
I think I finally gave up because it's become too much same-old, same-old. The different class stories were good in concept and mostly entertaining in reality, but once you've done them.. There's not much beyond the basic morpg grind-grind-grind-some-more. The expansion post-class storylines have had some interesting ideas, but have been rather spotty.