I really like the storyline. It shows the pain, challenges and decisions he must make. Yes, I think there are some plot holes.
1. The family, they are dead. Like the movie said, the replicas have a copy of the subjects conciousness, in other words, a copy of the subjects themselves placed on to a computer and made into an algorithm and placed back into a body. But the movie leads with they are reborn. If they are reborn, how could William talk to himself (replica) and make separate decisions apart from the real William.
2. Not a plot hole. Its been a long time, but they used stop-motion animation for the replica machine. If you have a movie like this, and can afford Keanu Reeves, you should be able to use decent CGI. But I am forgiving if the story is good.