All Star Wars movies have flaws. Actually all movies have flaws; just like all stories have flaws.
Lucas screwed up big time with the decision to film almost everything in a green or blue screen room with his latest movies. That's the major flaw the prequels have. Another problem is his choice or whoever picked some of the actors. Apart from that if you actually look at the original ones and then the prequels you'll realize they mirror each other. Or as Lucas himself said echo each other.
Actually the whole green screen/blue screen argument isn't really a valid one. The prequels actually used more practical affects than the originals. Episode I alone had more set pieces than the entire original trilogy combined. III was the only movie in the series to use more digital affects than practical. The originals also used a ton of blue screen. Scenes were enhanced using things like realistic animation and puppetry. It made sense to eventually replace these with CGI, most of the time it ended up looking better. Star Wars has always been on the cutting edge of special affects. In truth, many people often can tell the difference between what is CGI and what is real.