Apart from Anakin (annoying, clearly evil, little moppet) and Ja-Ja sphincter, Episode 1 is not too bad, but those are pretty big big caveats. The political manoeuvrings are the key features on the film: senator Palpatine/Darth Sidious manipulates the Trade Federation to blockade and then invade Naboo, forcing the lovely Padmé to initiate a vote of no confidence in the current chancellor of the republic's senate, who has been tied up in political protests from other senators (presumably under Palpatine's influence). Anyway, the upshot is, Palpatine gets elected as the new chancellor.
Episode 2 sees the next part of Sidious's plan snap into place. Under the leadership of Count Dooku (himself in the service of Sidious) the separatists (the Trade Federation among other entities) are amassing droid armies, forcing the council to vote Palpatine 'emergency powers' so as to be able to use the clone army that has just been discovered, conveniently complete (a decade after the order was placed under the name of a dead Jedi master).
What confuses me is: why does Count Dooku tell Obi-Wan that the senate is controlled by a Sith Lord (i.e. the truth)? If he is purely doing his master's bidding then it seems a bit of an unnecessary double bluff. Alternatively, does Dooku actually think he's fighting against a corrupted senate, his master's dual identity unknown? (after all, the separatist movement he extols would effectively constitute the rebel forces under Palpatine's upcoming Empire...)
Episode 3 then would be my choice for the label of favourite. This despite General Grievous being so easily separated from half his hands by Obi-Wan; the Cyborg was a Jedi slaughtering machine in Clone Wars the Animated Series. An excuse is that Windu injured Grievious's biological components as he was escaping with the abducted Palpatine, setting the scene for this episode. All the same I would have loved to see some of the Cyborg ass-whooping from the cartoons rendered with the realism of a live action film.
Dooku is unconvincingly bested by Anakin (after dispensing with and precisely pinning Obi-wan in the most trivial manner), presumably Sidious convinced him to risk parting with his hands, but was then surprised when Palpatine pressured Anakin to kill him (perhaps revealing Palpatine's true identity to Dooku for the first time?). [On reflection, I think they were just trying to mirror Luke's eventual triumph over Vader in Ep.VI, but this is one place where the older films actually looked more convincing.]
The best line in the septrilogy - “So this is how liberty dies...with thunderous applause.” - Padmé, as Palpatine uses the perception of an attempted Jedi coop to forgo relinquishing his emergency powers and instead transform the republic into an Empire under his control. If there is only one truly useful aspect of Lucas's Star wars, it is to convey to the masses the danger of liberty being stolen by those promising deliverance from fear. Which made it extra disappointing when at around the same time, the Bush administration got a second term, purely (it seemed to me) because the country was still 'at war' with some nebulous evil.
Anakin becoming Vader physically: losing his remaining biological limbs and more, in a cauldron of pain, ties the two trilogies together very satisfyingly. And at the hands of an Obi-Wan characterised as infinitely more likeable (compared to Mr condescension in Ep.2), every bit the loveable hero. On the other hand, Anakin's ultra-emo, angsty, whiny defection to the 'dark side' is pretty irritating to watch, especially with Hayden Christensen's cardboard style contrasting sharply against Ian McDiarmid (Palpatine) hamming it up, though maybe that's what they were going for... The implausibility of McDiarmid as a supple swordsmith (capable of slaying 3 jedi in the blink of an eye) eclipses Christopher Lee's (Dooku's) strained efforts (in Ep.2). He particularly unconvincing when sparing with a overly stiff Samuel L. Jackson, however maniacal McDiarmid's facial expressions.
“The Clone Wars”  CGI film is a pile of arse IMHO, but is the reason I ended up re-watching the Star Wars ark in order and writing this ramble.
The Original Trilogy: Yes I've lumped them all together; any insulted die-hard fans may bite me. For a start, episodes V and VI run together anyway (like Kill Bill Vol.1&2). And all in all there isn't much depth to the universe in these older films, it's all about a small bunch of pals blundering through to massively improbable victories. Presumably the clone/storm-troopers are now geriatric, hence getting their arses kicked by a hand full of furry midgets armed with sticks and stones (Ewoks, of course). Also, I'm sorry but, they look crap, in so many ways, compared to the recent films, and it does matter.
As for inconsistencies, I did pay as much attention as I could, and the only problem that could not be effectively explained away is that Leia seems to remember her mother. So she's either making it up or remembers being born; perhaps that is her special power, well and good seeing as the misogynists didn't see fit to provide her with a light sabre to waggle about comically.
Darth Vader's ultimate redemption also redeem the films. Although the attempt to have him exhibit complex wavering emotions while wearing a black PVC suit with full face mask and helmet is laughable. It's a strong motif that flies in the face of all the good guys / bad guys childishness.