I never had much of a complaint about the movies excluding the fart joke in the Phantom menace.
To be honest for some time I felt something similar and the fact that a fanedit like the TM2YC one can fix the movie means there is good in it. No amount of cut and past can save really bad movies like "After the last season."
However after a while I noticed that the comparison does not really hold, check this list:
Archetype: EpI, VS EpIV.
Master: Qui-Gon VS Obi-Wan. Somewhat fine, but in Ep IV Obi dies to help Luke; in Ep I Qui-Gon dies because he's weak and he looks fairly insane.
Student: Anakin VS Luke. Anakin is shown too much as a loser. Sure he is a genius mechanic, but he never finished a contest.. ect. Luke is not so bad and actually quite heroic on the Death Star.
Support: Obi-Wan VS Han solo. I think in this case we are fine. Both are fine.
Strange one: JarJar VS Chewbacca. Do I really need to explain?
In the fanedit everything is fixed because: any reference to Anakin being a bad racer is removed, he is a amazing pilot and the race actually works as Establishing Character Moment since the "child" shows an extremely serious and concentrated mode unusual at that age. JarJar now have alien speak with subtitles (and he does not say any nonsense), he is son of leader of his people, his stupid attics are removed and he actually meaningful and helpful.
Since everyone is better Qui-Gon, while he still dies because he's weak, does not look insane. Trusting Anakin and keeping JarJar nearby now make sense.
Similar comments apply to Ep2 and Ep3.