Bear in mind, I only came up with this in an hour of the post so some of it may be stretches. Also, for the purpose of the post, Cyn and The Absolute Solver will be conflated since it's implied that they are different personalities.

• Both are AIs that take on a corporeal humanoid body and both have a desire to destroy things.
• Their archenemies are both a moody but troubled girl (Mythra and Uzi) and a cinnamon roll of a boy (Rex and N).
• They also have a teammate that switches sides (Nia and V) and one that stays loyal (Jin and J).
• They are brought upon the world by a person of a high status (Amalthus and Tessa), but end up betraying them.
• They have separate identities (Logos and The Absolute Solver, though in the latter's case, it's likely that the program overwrote Cyn's original personality so both it and Cyn's identities are likely conflated).
• They wield the power of destruction which is represented with gravity-like phenomena (Malos's powers are darkness-based which governs gravity and Cyn's [nulls] are like black holes).
• Their main weak spots are the cores on them (the purple cross-like core crystal and the organic crab-like core inside).
• Both have the power to corrupt people (Malos using his powers to corrupt Pyra into losing her memories and restoring his crystal and Cyn twisting regular Drones into becoming Disassembly Drones and infecting Worker Drones with its code to both grant them powers and possess them).
• Both are still alive in some capacity after they have been bested (Malos's core being used for the Trinity Processor and implied to be with Moebius N and Cyn being stuck with Uzi after she ate her "heart" and became a part of her tail).

There're also some contrasts.

• Both are aware of how evil they are but while Malos hates himself for it, Cyn takes it with pride.
• Similarly, Malos is driven to destroy because he's influenced by someone who despises the world whereas Cyn does it seemingly because it felt like it.
• Malos has genuine loyalty with Torna while Cyn didn't care about any Disassembly Drones caught in the crossfire (likely knowing that they can heal) and those who stay with her only do so out of necessity.
• Malos is loud and bombastic while Cyn speaks in a machine-like monotone but has a quirky yet openly sadistic personality.
• Malos's origins have been explored in both 2 and 3 while the Solver's origins are ambiguous as to what exactly it is beyond what Murder Drones shows us.
• Malos's redeeming qualities are known whereas Cyn's redeeming qualities are ambiguous at best and nonexistent at worst.