Fully C.G.I. Jar Jar Binks		1. OVER-FLAUNTING C.G.I. TECHNOLOGY I have nothing against computer animation, (I'm a professional computer animator myself). But I feel that Phantom Menace depended too heavily on the "tricks" of Industrial Light & Magic instead of great storytelling, Jar Jar most of all. To test, imagine each scene that he is in without Jar Jar and the scene still works. Many fans found Jar Jar particularly irritating to watch.
In the previous trilogy (Episodes IV-VI), the comedy-element was provided by R2-D2 and C-3P0. But in addition to their "comical-ness", R2 and 3P0 were an integral part of the plot and as such had many "non-humorous" moments onscreen. The comedy element in Phantom Menace however (Jar Jar), acts more as an annoying side-show from the plot, thrown in as an afterthought to "lighten the mood". Although it should be noted that a great deal of Jar Jar's irritativeness is Ahmed Best's obnoxious voiceovers. (Lucas shouldn't have used him!)
Being a computer graphics professional myself, I attest that "organic" computer-generated characters still do not quite hold their own against the more traditional foam-latex masks, prosthetics, and makeup. As lifelike as lighting, mapping, and motion-capture get, character-animation still looks "computer-generated" to some degree and dates itself very rapidly. Compare the classic Terminator with the computer-effects-heavy Terminator II, and you will see how the sequel ironically appears more dated now.
...and speaking of, when are the folks at Lucasfilm going to stop computer-generating Jabba the Hutt, considering that the original lifesize puppet of the character created for Return of the Jedi looks a thousand times better?!

		2. THE BOY WONDER Probably my biggest complaints are to be found with the young Anakin Skywalker. Contrary to popular opinion, I do not believe it is Jake Lloyd's fault. The screenplay has the young Anakin simply too good to be true.
It is far too unrealistic for Anakin to be: An expert inventor-mechanic-scientist, A super-daredevil stunt pilot winning a dangerous race for his life and freedom, Have super force powers even greater than Yoda, and have a generous heart of gold to boot, ...ALL AT THE TENDER YOUNG AGE OF NINE!
More emphasis should have been placed on Anakin's potential to eventually fall prey to his anger and pride. The fact that many "non-Star Wars fans" never connected the little star of the movie with Darth Vader of the earlier installments is proof of this. In a pivital scene within the Terry Brooks novelization, young Anakin breaks out into fisticuffs with a Rodian youngster and lets his anger get the best of him. This short but important segment should have made it into the film, as it gives a hint of how Anakin cannot control his anger (as Luke himself eventually had to learn to do), or else be lured to the Dark Side. It is a grave mistake to tell of Anakin's fall as if he were completely an innocent victom. What about the inherent "dark side" within each one of us, and of free will; (the ability to CHOOSE to be either good or evil)? Lucas obviously wants us to love Anakin as we loved naive young Luke, and that is a mistake!

the many faces of Master Yoda		3. WHAT HAPPENED TO YODA? No one can tell me that the Yoda puppet used in The Phantome Menace is the exact same one used in The Empire Strikes Back, (...unless because of time, the puppet had to have some serious plastic surgery to be usable after 16 years of shelving).
His eyes are much larger and the irises of his eyeballs are much lighter and more assertive this time around. His brow is also much more pronounced and his nose is upturned and more "pig-like". The wrinkling furrows upon his scull are ironically more detailed at this younger stage than in Empire. Adding thicker hair was also a stupid idea. (30 years to Yoda would be the equivalent of about 2.5 years to you & I). "When over 900 years old you reach, no visible difference will only 30 years back in time make."
Also, why does Yoda seem so emotionally tense and aggravated in this Episode when he is so tranquil and stoic in the earlier installments? He seems to have very little of the inner-peace and tranquility, self-control or Toaist wisdom that he emanates in Episodes V and VI. He comes across as that one obstainate asshole in every office meeting who likes to hear himself loudly pontificate rather than a spiritual guide to the Jedi Knights.