It just seems like because G1 Makuta is evil, most people assume G2 Makuta is evil.
But he's not evil. Just misunderstood.
Like these guys.
Anyways, it clearly states in The Legend that the Mask of Ultimate Power took control over Makuta because it was too strong and dangerous. In JTO, Narmoto clearly states that the MoUP made Makuta "dark and evil".
But another interesting fact is that Makuta is the only Okotan that has purple eyes (as far as we know of 2015-2016 anyway). The only eye colors we have seen on Okotans are blue, red, and yellow.
So what makes Makuta so special that you give him purple eyes?
In speculating an answer for this question, I examined how he and Ekimu could be brothers. Are they brothers-in-arms brothers, or literally brothers?
ASSUMING that he and Ekimu were literal brothers, they could/should share the same eye color, not to mention have the same elemental color.
So how did he get purple eyes?
He became corrupted by something evil, though he was not consumed by it enough to immediately start thinking about killing Ekimu. Instead, he become jealous of Ekimu's accomplishments and makes the MoUP.
Red + Blue = Purple
Evil overpowering good equals corruption.
Also, who could have corrupted Makuta?
There is only one element which seems to be evil and that is shadow. And who is the embodiment of shadow in G2?
Umarak the Hunter.
And (speculating) where did shadow originally come from in the entire Biological Chronicle?
The Mask of Shadows (Kraakhan) of Makuta Teridax!!