(Halifax for the win. Is Bubbles back from Monkton with the tanker yet? :) )
E Pluribus Neo's main philosophy and goal has mostly been for the freeing of bluepills from the Simulation and the protection of those who have already been freed, to a greater extent than Zion, especially of the former agenda. As with all organisation, however, there are a spectrum of ideologies and how they are applied, within this.
The Cypherite movement on the other hand has traditionally focused moreso on the protection of bluepills and, more recently, the stability of the System, if not only as a means to this end. How this is achieved, however, varies vastly from Operative to Operative aswel as the differing styles and methodologies of Veil and Cryptos. The group's mission controller and leader, respectively.
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As for Marcus' possible alignment, I'd see most striking the consideration of:
His meditation and alternative lifestyle:
Perhaps Zionistic in nature as a plethora of traditionally Eastern religions serve as a fundamental founding for the original Zion philosophies, in my personal opinion. While the practice of meditation stems from these religions and beliefs on the simplest level, his additional journey toward finding himself and a true understanding of everything around him (the Universe) - to "free his mind" so to speak is a very fundamentally Zion.
His appreciation for the natural beauty around him:
Could be translated as a desire to protect it, once he comes to term with how the world around him is constructed (and maintained) and the threats made to it on a daily basis - a strong attraction to the avenue of working with the Machines for more than a few Machinist operatives.
His seemingly subconscious desire to reproduce this in a form personal to himself:
Could be seen as a desire most in tune with the general concensus of Merovingian operatives: moulding his surroundings, and possibly himself to an extent - the fabric of the Matrix's code, to a shape he finds personally pleasing.
... while this analysis is remarkably simplistic and basic - on one level - it does, on the other hand look at key aspects of Marcus's personality. That which is most important to him and core to the essence of his being.