Problems with the humanistic message
A problem I have with the remake is it tries to justify humanity's rebelling against the gods by portraying them as oppressive tyrants when they do not come out that way.
1. The gods are not shown to be that bad.
Zeus is repeatedly shown to be loving and merciful to mankind. He aids Perseus. At first he only humiliated Calibos instead of destroying his entire city outright as the other gods wanted. He has allowed mankind to grow strong enough to become independent and only takes action when the gods' lives are threatened. He spares Argos after the Kraken is defeated. The only real complaints we have are some of the male gods sleep around with some mortal wives and Perseus' adoptive father is having a bad run at fishing. Oh, and Io was cursed to be young and beautiful forever instead of being cursed to live forever as old and ugly or any number of other things. The gods come off as kind of jerks, but not oppressive tyrants.
2. Mortals do not come across as any better or perhaps worse.
The well-fed nobles of Argos decide to hold a celebration and only Andromeda remembers the hundreds of dead soldier or considers possible retaliation. It hardly looks like people are starving.
Years earlier, Calibos decided to attack Olympus for some reason...and murder his wife when Zeus humiliated him instead of outright destroying him.
Perseus himself is more interested in vengeance on Hades and being a "man" than in the lives of his comrades or the city. His selfish refusal to use his divine gifts gets his fellow soldier killed.
3. Man claims not to need the gods or their gifts, but only wins thanks to them.
This may be the biggest problem. Perseus wants to do things "as a man" and mankind itself claims not to need the gods and that they "are the gods now." Yet, Perseus only overcomes his challenges and defeats the Kraken by relying on gifts from the gods: the sword, the horse, the strength, even Medusa' head all come from the gods. Without all of that he would never have defeated the Kraken. So he needed the gods and could not win "as a man."
Maybe it was the reediting done by the studio, but the whole plot falls apart with unlikable characters and mixed messages. The original at least lacked these massive plot holes.