When Medusa has the Djinn in her grasp and can't kill him is she having an Oh, Crap! moment or is she just shocked and acting emotional about that someone isn't turning to stone when she looks at them?
Aphrodite's cursing of Medusa in the first place. Was it an example of Jerkass Gods? Or maybe in her own way she felt she was helping Medusa out - giving her the power to take revenge on men who would try to wrong her. Medusa retains some of her beauty in this version.
If you've never seen the original you might be asking yourself what a futuristic robotic owl is doing laying in the bottom of a trunk in ancient Greece.
The conversation that young Perseus has with Spyros about his anxieties regarding the new baby and Spyros not being his biological father. It has no bearing on the plot except to set up a character who is killed a few scenes later without so much as a single line. It makes more sense with the original ending where Perseus rejects Zeus and says that his real father is a dead fisherman (the moral being that blood ties mean nothing without a familial bond). But with that plot point dropped, it does seem a tad random.
Designated Villain: Medusa again, with a deeply tragic backstory. Io even seems to think she deserves pity. Of course, she's more of a means to an end to defeat the real villain, but still. Although here she's shown to be far more malevolent than her counterpart in the 80s version — where she appears to take great delight in killing the soldiers, and cackles whenever she successfully scares them.
Ensemble Dark Horse: Alexa Davalos's Andromeda. Despite the backlash from fans of the original, when the first trailer was released — response to Andromeda's "have you seen what's happening out there?" was very positive.
The Scrappy: Io is this to fans of the original, for being Perseus's love interest instead of Andromeda. What's more is that Alexa Davalos's performance as the latter was one of the things fans reacted positively to, so Io being the love interest left a bad taste in fans' mouths — especially with the news that she was shot as a platonic figure to Perseus at first and then retconned into being a love interest.
Strangled by the Red String: The alternate ending from the Blu-Ray is closer to the original in that Perseus and Andromeda fall in love... even though they barely share screentime together due to Andromeda being Demoted to Extra, Perseus is a Darker and Edgier hero than the "motivated by love" original, and the rest of the movie builds up a different love interest in Io. This is due to Executive Meddling finding Io as a better love interest, cutting most of Andromeda's scenes and re-editing Io from a platonic figure to a romantic one.
Poor Bubo, often regarded as The Scrappy is reduced to a cameo, and a rather callously offhanded one at that. This is because Sam Worthington hated Bubo and kept complaining about it until the director removed it almost entirely to appease him.
Loads of characters had bigger roles that were cut down in editing. Apollo and Athena played a big part in the plot, scheming against Zeus. In the final film, Apollo only gets a couple of lines in the first council scene and Athena is Demoted to Extra. Likewise Alexa Davalos delivers a good performance as Andromeda. But most of her scenes were cut. She at least gets a larger role in the sequel.
The first draft of the film was completely different: it mixed several mythologies, and it had Zeus, Thoth, Marduk, Osiris and even Yahweh going against Tiamat and her followers, while Perseus had to join forces with an Earth goddess Love Interest to fight a human cult of Tiamat led by a priest named Fantasos. Even if it was guaranteed to be a religiously controversial film, there is no doubt it would have made a really interesting story.
There were times when it felt it they were setting up to deliver the message "just because they're your children/you created them doesn't justify abusing them," but it never happened. Arguable, however, as Zeus seems to come to a realization along those lines by the end: if the gods hadn't been so hard on the mortals, the mortals never would have rebelled, and the stage for Hades's takeover would never had been set.
If one goes by the behind the scenes notes, the final plot was actually going to be quite interesting, with Athena and Apollo essentially scheming against Zeus, and Perseus's comrades getting more character development. For whatever reasons it was heavily cut down into a rather simplistic revenge plot.
Liam Neeson as Zeus gives it his all and as usual he's probably the best thing about the film.
Alexa Davalos as Andromeda was one of the few things fans of the original thought was good about this, and some even felt she was better than the original Andromeda. Too bad most of her scenes were cut.
Unintentionally Unsympathetic: Zeus is this in the final cut of the first film. This is primarily due to him being an antagonist initially but Executive Meddling trying to make him more heroic. So he has an abrupt change of heart and decides to help Perseus. This is after he's already ordered the Kraken on Argos and it's said he raped Perseus's mother.
If Hades hadn't gone out of his way to be a dick by killing Perseus's family, he would have been able to pull off his plan to seize power without a hitch.
If the Harpy that stole the bag with Medusa's head in it had, say, dropped it in the sea, or fed it to the Kraken, Hades would have won straight off.
Or they could have turned right around and, you know, used it on Perseus. Just saying.
If Perseus had just gone with Zeus when he asked him to in the sequel, he probably could have stopped Ares and Hades from imprisoning Zeus in the first place. What's worse is that he makes a big deal out of not leaving his son's side...and then five minutes later, leaves his son's side and a Chimera attacks his village, nearly killing the both of them.
Guys...just leave Argos before the Kraken shows up.
RiffTrax: Don't skip town or anything, that would be cheating.
Visual Effects of Awesome: Painfully averted with the slapped on 3D, but the Kraken looked freaking awesome. It's a shame he was only there for less than five minutes. For those watching the film in 2D however, the CGI is exceptional.
To make up for the first film's Nonindicative Name (there were no Titans to be seen), Wrath has a story revolving around the resurrection of the Titan Kronos.
Big-Lipped Alligator Moment: In the sequel there are a couple of times in the Labyrinth where Andromeda thinks she sees Korrina walking around and Perseus sees Helius. There is a line from Hephaestus referencing possible hallucinations — but it's not drawn attention to that much. Also when Perseus is separated from the others, he's attacked by a minotaur. After he kills it, it's not mentioned again and there are no other monsters put as obstacles in the Labyrinth.
Complete Monster: Ares, the god of war, is the disloyal son of Zeus, who sides with Hades as the Titans awaken. While Hades is motivated by his fear of death and ultimately redeems himself, Ares is completely unrepentant and is Driven by Envy of Zeus showing favor to his demigod son Perseus. Ares and Hades sell out Zeus and the other gods to die to awaken Kronos in exchange for being spared, during which Ares needlessly beats and tortures Zeus in captivity. Ares later kills some of his mortal followers, impaling and tossing aside a devout worshiper who prayed to him for salvation and tried to appeal to him. When Zeus manages to reach out to Hades, Ares immediately tries to kill Hades and proceeds with awakening Kronos to wipe out the world, mortally wounding Zeus in the process. During the final battle, Ares takes Perseus's young son Helius captive intending to force him to watch as he kills his father.
Critical Research Failure: The Chimera has wings, which would have been cool but misses out one important bit of the myth: the reason Bellerophon had to go through all the trouble of capturing Pegasus so he can fly above the monster, safe from its flames and fangs. This would, quite logically, not work if the Chimera could fly. The filmmakers clearly went for Rule of Cool.
Strangled by the Red String: Perseus and Andromeda kiss at the end. They hadn't really had much in the way of romantic development, aside from clear tension when they first meet again. In the movie's defence it's entirely a Maybe Ever After situation. Likewise a third film was planned, but eventually dropped, so presumably the romance would have been developed a lot more in that.