The biggest problem with TOR is that they have not explained how the Jedi Order was rebuilt after the Jedi Civil War, and more specifically, the First Jedi Purge. It's as if the war was nothing more than a small skirmish, a footnote in history, while as we saw in TSL, the war brought the Republic to near death. That also brings up the question of what happened to the Exile's companions. After all, they were supposed to rebuild the order, and as of now, that has been totally ignored.
What perplexes me most, is the fact that BioWare has been continuously using Mark Griskey's score for TSL in their media, which seems to negate their retconning of K2. I mean, if they want everyone to overlook TSL, then they should keep mum on the subject entirely.
If Obsidian wants to do K3, then by all means, give them two to three years, more funds, and a larger development team, and they'll whip a product that will be on par with BioWare's polish, but have a much better plot and C&C than BioWare has ever done.