Here are the obvious reasons, and we could expand on some of the less obvious ones if you want...
1) Manannan has no trouble killing Alexander in KQIII. This would NEVER happen based on the new storyline introduced in TSL. Alexander gets killed if you wait around too long and don't get into any trouble even so you can't claim he only kills Alexander in moments of rage either.
2) In KQV one of the big threats made by Shadrack is that he is going to feed the Royal family to Manannan, starting with Valanice. This makes no sense either given that according to TSL Valanice is Manannan's daughter. There is no way that he would feed Manannan's daughter and grandchildren to him. This makes no sense either.
To me, those two things are in direct conflict with the plot of the original games.
As for taking the game in their own direction, that is POS's choice and I can't say much to what they wanted to do. It is their game and they can do what they feel makes sense. People are going to love it, hate it, or have little opinion. I personally think it goes against the originals. That by itself does not make the game bad. It just means they went away from the facts previously established in the series. That is why I wonder what Roberta would think now. Everyone here was so quick to use her comments on episode 1 to defend the game, I wonder if she would say the same things now or once the game is complete. I personally think that she would not have such high praise. I doubt she would agree with the direction of the story.