Ok, without turning this into a "bash the PT" thread, I will continue with the thread's topic -- how the PT changes the OT for me. I really mean that I don't want to be overly critical as well, I know for many it is beating a horse.
I think the number one issue I have is how small the Star Wars universe became. This may seem like an odd statement especially considering we see so many different planets and cultures in the PT (and now the SE ending of Jedi); but it isn't the worlds I am speaking of but rather the characters. The introduction of Greedo, C3PO, Chewbacca, etc; just felt like a desperate reach to me. I don't think that Lucas needed to have any continuity beyond Anakin, Obi-Wan and of course Palpatine. The PT would have been much more powerful had it shown the golden age of the Jedi as an era removed from the OT; but for me it felt like Lucas was trying too hard to bring two generations together. I think had the story been told as I would have done so, there wouldn't have been a lack in reception; Star Wars is in and of itself impacting enough. Of course the introduction of fart jokes etc, didn't help anything in that respect either.
Aside from that, I have a very difficult time with the PT because of the effects, and while many here might prefer modern CG, for much of the films; I found it dodgy at best. I know that the effects of the OT are nothing staggering by today's standards, but I'll take the Cantina Band aliens anyday over how unrealistic the Geonisis termite crew looked. Sometimes puppets just look better.
Again, I don't want to start a war here, but these are at least a few of the things that come to mind.