With the advent of it's aligned continuity the nature of the war between the Autobots and the Decepticons changed. No longer was it simply Megatron the warmonger wishing to claim rule over cybertron or whatever, but conflict born of inequality and the desire for change in a rotten system (I'll be focusing on Prime and ONE for the most part but I believe this holds for all works within the aligned continuity). Under this new continuity Megatron is a bot born into the lower casts of cybertronian society. In prime (one of the first shows featuring the new aligned continuity lore) he's a gladiator with no name till he's christened Megatron by his fans, a name derived from the prime Megatronus due to their sharied strength and ferocity in battle. As a gladiator of great fame and stature yet still a member of the lower cast, he uses his potiton to bring attention to their troubles and treatment. Doing so he enters the world of politics where he meets and befriends Orion Paxs (pre matrix Optimus Prime) a data cleric. The two desired the same thing, equality for all bots on cybertron. But they differed on how to make this happen. Orion desired to change the system from within, while Megatron desired to destroy the currenty system and create a new one. When the chance presents itself the two present their ideas to the high council where they choose the Young Orion Pax's idea over Megatron's. Thus dividing the two and eventually sparking the war between them.

Transformers one even has the two both apart of the lower cast, they journey together and yet differ on how to simply move forward (they're obvioulsy not the same person, but they struggle to even see eye to eye). D-16 wants to KILL Sentinel Prime after learning the trouch (Man had his world destroyed in a day), where Orion wants him to face justice (Won't lie, Sentinel should be tried of course, But I don't think D-16 is wrong for wanting to kill the person that's confined him to a life of slavery upon birth, created a system where bots like them, Miners had no mobility / power, and killed the 13 Primes for power all to end up serving energon to the quintessons. Something that does not flow freely anymore due to his actions). After finally killing Sentiel he processed to destroy everything around him, tearing down all Sentiel has built, desiring to create a new system in its place (He will no longer be lead by false profits, He will be his own leader).

This is realitivly the bases for the aligned continuity, greatly simplifying you have Optimus and Megatron who'll desire the same thing then differ on how to execute.

(Now I'm somewhat of a villain apologist, I mean some of them just have good takes, but their executions got me acting like a stranger) Aligned continuity Megatron is sympathic, he becomes someone that you can get behind. He's more radical when compared to Optimus but that isn't bad. In fact in something like transformers prime where the high council choses Orion over Megatron, I'd say that's just the council attempting to retain their status. The system is flawed and is built off the oppresion of others innately. When two bots come to confront those who sit on top to better their society why would they go with the one who's ideas would lead to the potential loss of their power and status. Orion is the safe bet for those of the high council. What he asks does not threaten them, all the while it can be delivered upon by bringing empty change. "Making the changes demanded" without ever changing a thing. Allowing people to believe that their needs are being met. I have to imagine that when Megatron desired to replace the system, something like this is why. The knowledge that changing it won't be enough, the reality that the system is not meant to be changed.

The inital ideals of Megatron in my opinion is justified, again he himself is a victim of a system that'd keep him underfoot, to never be seen or heard of. The fact that people know who he is, is an abnormality. His desire to replace their system with a new one I feel can be read as a power move, one where he simply desires to put himself on top. This is especially the case when you look at what he's became. Even so I'd say that isn't his intention, he simply recongnises the issues of their system, its too rotted to contniue as is. For the reason that when he's overlooked for Orion, he grows fustrated. It's not just jealousy, he recognise like I've mentioned before that to the council Orion is the better pick. Them choosing him a bot that's of a higer cast than Megatron, one closer to them is beneficial. Seeing this as proof of his beliefs about the system.