Worst: either case 1-4 or the last case of miles investigation 1.
It's not because they are bad written or anything(in fact, I would say the opposite), but, for me, they are just way too long and, because of this, are the only cases that made me genuinely bored.
I like them, just less than many other cases
Best: absolutely case 4-4.
I just love how we finally get to investigate and see what happened seven years before the events of the game and how everything went so well together.
Plus
May I ask what are these plot-holes, if It doesn't bother you?I ask this because I'm not that expert regarding writing, so, to me, even the most basic story looks good and I can't notice the plotholes present in a story, unless they are really, REALLY obvious.