I think they decided to remove the EU for one large, furry, reason. Chewbacca.
Had they followed with the EU as canon, time would need to be devoted in this first film to explain why Chewie was dead to all those people who haven't followed the various novels, etc. Once they'd made that decision it makes sense to then cherry pick what they want to keep. Likewise I wouldn't be surprised to not see Mara Jade as Luke's wife now, despite the fact that I think she's been a great character.
I'm also a fan of the prequels. I think that Episode 1 was always going to be very difficult as it had to set up new characters, existing characters in new scenarios, and set up the political background over which Palpatine maneuvered in order to get himself into power. That doesn't really set itself up for an interesting story, but it does set up eps 2 & 3.
Beyond this, if you delve a little deeper, Lucas did something very interesting in the story telling, beyond the parallels that most people will spot. It's a very deep discussion, so I won't try to explain too much, but if you have some time to spare, have a read of this article as it exposes a far more complex bit of story telling than is first apparent:http://www.starwarsringtheory.com/ring- ... -prequels/
Put simply, it's fairly clear that episode 1 is a parallel to ep 4, ep 2 to 5 and 3 to 6, particularly with Luke's journey as compared to Anakin's, but the reverse is also true, with 1 and 6 echoing one another and 3 and 4 also. It'll mess with your head, but when you start looking at corresponding screenshots from the various films, it all seems to make perfect sense.
Although Lucas hasn't talked about this style specifically, it's well known that he constructs his stories with a complexity far beyond mere beginning, middle and end...