For me, the fact that Bioware/LA developed a game within the overall KOTOR genre but was not a KOTOR III says to me that any remaining likelihood of a KOTOR III occurring is greatly diminished if not destroyed entirely. Which means that we will likely never get a physical manifestation in RPG video-game format of what happened in the storyline immediately following TSL with regards to Revan, the Exile, and the party characters from the first two games. I would sort of compare it to reading the first two Tolkien novels in the LOTR trilogy with the third book never being released. I never got to experience the end of the arc, and never got any sort of closure. Although TOR does not have much to do with this lacking of closure directly (except for the tidbits of info on the Exile and the scenes with Revan) its mere existence in my estimation is a reminder of how I will never see that closure.
Besides those feelings, I also dislike TOR because of its MMORPG format. I'm a KOTOR fanboy, and I like to think that the story I developed playing KOTOR and TSL was as much uniquely mine as possible. That feeling gets lost (at least to me) somewhat when completing a quest I see another real player in the game, especially when they have a vulgar screen name (ex: something like...luvs2splurge; well this is not that vulgar but I think you get the point). This occurs a lot, especially during my short tenure playing WoW. That atmosphere makes the game feel arcadey to me and lessens the experience of the game. It serves as a reminder that this is not a thrilling story that I'm creating with my choices and actions, but just a video game filled with other real people doing the exact same thing. Obviously, with every video game this is the case, but I don't see that when playing RPG's like Skyrim, KOTOR, Mass Effect etc. The only characters I encounter are NPC and the only real person they react to is me. For a story-driven game, I prefer that dynamic.
I've never played TOR, it might be a very good game on its own merit (as proven by the many who play it), but for what it does to the canon of Revan and the Exile, and because it is a KOTOR game in MMORPG format I dislike it.