Among all the characters in Voltron: Legendary Defender, Prince Lotor appears to be the most morally complex and torn, since he is half-Altean and has a connection with princess Allura. In the end, however, he was just a villain. Even when he temporarily on the heroes' side, he was still ultimately a villain who tricked, betrayed and exploited nearly everyone around him. Not even his mission to restore the Altean people or to destroy the Galra Empire can balance that out.
Exploiting The Alteans
A major strike against Prince Lotor is his intentions with the Altean people. It is true that he spared a few thousand Altean colonists from the wrath of his father Zarkon 10,000 years ago, setting up a safe, isolated colony where the Alteans could live in peace. Lotor was sympathetic to his Altean heritage and wanted a better future for his mother's people. The problem is that his methods quickly became extreme, and were cloaked in cruel deception. He used the colony as a testing ground to see who had sufficient levels of quintessence, and those Alteans were lured away on the pretext of going to a second colony. Lotor harvested them to gain more quintessence, believing it would give him the power necessary to restore the Altean people.
Allura knew this was terribly wrong. Whatever the Altean people's future would be, it would not come from lies, sacrifice and exploitation. Heroes sometimes make sacrifices to restore good in the world or defeat the villains, but not like this, at the cost of innocent lives. This turned Allura and the Paladins against Lotor, and once he was in the quintessence field with Voltron, Lotor went mad and exclaimed that he would become all-powerful without Voltron's aid and create a new Galra Empire in his own vision. He thought of it as a future for the Alteans, but in reality, it was a future for no one.
Not even the sacred Oriande, the heart of Altean alchemy, is safe from Lotor's machinations. He wanted to visit it not to help Allura restore the Alteans for their own sake, but for the sake of his schemes. He wormed his way into Allura's mind and used her to access Oriande, but this scheme failed when the white lion guardian rejected him as unworthy.
Galra Empire Machinations
Lotor isn't necessarily sympathetic in the context of the brutal Galra Empire either. He might oppose his father Zarkon, but he also opposes his mother Haggar/Honerva as well. At first, Lotor looked like a ray of light for the Empire -- he wanted to work alongside subjected races rather than exploit them, and he didn't want Voltron destroyed. In the end, however, he was simply a different flavor of his father. He wanted power above all else, no matter how he tried to spin it, and while his ruthless streak was less brutal than his father's, it was more deceptive. In short, Zarkon's evil was a great roar, while Lotor's was a quiet knife in the back.
He even tooks his generals (Acxa, Zethrid, Ezor and Narti) for granted. They were pawns to him, and he created a web of both false and real betrayal to juggle them, Voltron and the Galra Empire in his scheme. His generals turned on him more than once, and Lotor willingly sacrificed them as part of his schemes. By the time he had assembled the Sincline ship, he was operating it alone, and Acxa had actually switched sides to Voltron for good. She couldn't stand working with a self-centered, lying backstabber like Lotor. It is clear that Lotor has no friends except himself, and that makes him a fascinating but unsympathetic character, no matter what idealistic speeches he makes.