Definately having Anakin as a little kid for the whole of Episode I was the first really big mistake by GL. If it has to shown how he was found by Qui Gon (or better yet, by Obi Wan) make it happen in the first 15 minutes to half hour, then move onto when he's an adult, let the audience get to know the character as he will be for the rest of the trilogy in that first film.
Of course making adult Anakin so unlikable was probably the biggest mistake of the PT, impossible to build a story that anybody will care about around a character that nobody likes. That was the real nail in the coffin for the Prequel Trilogy.
The Phantom Menace is easily my favourite film of the PT because little Ani at least you can kind of get behind, he's not unlikable at that point, just a little annoying at times with his exclamations like 'Now THIS is pod racing!'. Liam Neeson is the best thing about the film of course, he adds much needed class and gravitas to proceedings in his role of Qui Gon. The Darth Maul fight is easily the best of the prequels for me, the pod race is actually pretty cool and the real clincher for me is that it was shot on film so it has that Star Warsy feel, it feels like it belongs alongside the OT. The second and third films shot on digital by comparison look incredibly fake and artificial, lacking that organic lived in feel of the OT and TPM.