Yes there too many incongruities and plotholes to be ignored between the classic trilogy and the prequel trilogy. HOWEVER, there is a very good reason for this (one that a lot of people seem to ignore or forget).
You have to remember when the original movies were made. When George Lucas made the first trilogy, he didn't know if he was ever going to make the sequel/prequel movies. He wasn't even 100% sure he was going to be able to make "The Empire Strikes Back" and "Return of the Jedi". What if "A New Hope" had tanked in the theaters and Fox wouldn't greenlight the two sequels? He had to make a movie with the least amount of confusion for people to watch.
That's why you don't see any references to Qui Gon, podracing, Darth Maul, midi-chlorians, etc. Can you imagine Obi Wan mentioning to Luke, "Yeah I remember how I met your father. He helped get Qui Gon, Padme (your real mother btw), R2D2, and me off this planet by podracing. Oh did you know midi-chlorians live within you and help you communicate with the force. How do I know this? Qui Gon can sum it up the best. He's my former master whom I was an apprentice under. He's also the ghost that's been my company for 20+ years ever since I brought you, YES YOU LUKE, to this very planet! It's unfortunate he had to die though. He was killed by Darth Maul, a Sith with a double-edged lightsaber." You can see the mass amounts of confusion this would cause. He had to make "A New Hope" act like a standalone movie. Lucas had a little more freedom with "The Empire Strikes Back" and "Return of the Jedi" but people could watch the original trilogy and not have too many unanswered questions.
Now that Lucas knows that people are actually interested in Star Wars, he has free rein over creativy/complexity of the Star Wars universe. He can introduce characters, concepts, etc at will because he can always explain them later on if he chooses. This is evident in the prequel trilogy as he mentions characters we never see such as Sifa Dias (the one who ordered the Clone Army) and Darth Plagus.
Watch any movie with several sequels and you will almost always see that the first movie fits a mold in that they work as standalone movies and don't leave too many moviegoers bewildered after leaving the theater. The sequels are the ones that try to add more depth, mystique, and questions to the franchise. Look at movies like the Matrix for example. The only multi-movie franchises that don't fit this mold are the ones that are 100% sure that there will be sequels. The Lord of the Rings trilogy is a perfect example.
The only thing I can fault Lucas on is that some of the explanations in the prequel trilogy seem forced. Almost like he was trying too hard to tie the trilogies together. Including Chewbacca in Episode 3 is a good example. But like I said again, he couldn't include this information into the original trilogy as that would be too confusing for moviegoers.
People who complain about loopholes and the people who try to excuse those loopholes with crazy explanations need to know that sometimes not everything can be or should be explained. It's sometimes better to just let it go. The last thing I need is 10,000 Star Wars fans giving me 10,000 different reasons why Obi Wan doesn't recall R2D2 or why Princess Leia recalls remembering her mother (even though she died giving birth).