Oh, I have no doubt that it portrays problems in the order; I was more referring to the general depiction of the story. However, you cannot deny that the Jedi Order are once again "the good guys." Rather a fast transition, to go from the Jedi being few and corrupt to many and largely good again (and yes, I understand that it takes place several hundred years afterwards, but this is just an excuse to ignore previous plot developments and characters when it suits them).
KOTOR was hardly predictable, with it's rather excellent plot twist. Though you're most likely referring to how the main plot is rather predictable, how we are going to destroy Malak. Well yes, of course. An entertaining story requires confrontation (and usually defeat) of the antagonist. I guess if you perceive the story at a birds eye view in TOR, you look at the basic structure (who does what and when), the story is excellent. The same can be said for the first three movies in the trilogy (for the most part). If you consider the stories themselves, and not simply how they are told (such as important information being left out or characters making stupid decisions), the plot of the fall of the Republic is fascinating.
Episodes I, II, and III are still awful, however. When actually viewed in their entirety, with no EU or metathoughts to back them up, the narrative quickly crumbles. Why was the shield generator shot through the shield? Why was their a blockade earlier, but none now? Why does Qui-Gon only make stupid decisions? Why did the shapeshifter try to kill Obi-Wan, not part of her job, rather than leave?
The same can be said of TOR. From what I noticed, the narratives held up well enough, but every other part of them failed. The graphics and animations are lazy, the NPCs cookie cutter images of each other, the dialogue hilariously silly, and the dialogue choices ludicrously limited.
I will admit, I didn't play through all the characters. I got moderately far in the Agent and Bounty hunter playthroughs, and the experience was rather telling. The game was painful to playthrough, the copy and pasted fights of one to two button mashes, with silly cutscenes where I can choose to be GOOD or BAD and nothing else were frustrating.
Although, contrary to what I said, some of the plot lines were the most asinine things I'd ever seen. Like everything touching Revan. You're telling me, that the Exile (who defeated Nihilus) and Revan, could not defeat the Emperor, who was essentially a less powerful Nihilus (He had to do some complex ritual to eat a world). In fact, the Revan book provides a good idea of Bioware's priorities. Kill off the Exile and keep Revan alive for hundreds of years.
And just because some threads are split between characters, it doesn't mean the game is deeper. I think that's more of a ploy to ensure players would pay to play longer what was initially a subscription based game, so they could see all in the story.