First, it should be noted that I love the Silverio series, regardless of its flaws.  I see those flaws, I recognize them, then I shrug as I realize I don't give a flying fart about how the critical part of myself feels. 

First, lets consider the two games that have come out (so far, given that the setting is so insanely detailed that it would be sad if they didn't make more games) in the series separately. 

Silverio Vendetta

Silverio Vendetta follows Zephyr Colerain, an unemployed deserter with an inordinate fondness for alcohol accompanied by an inability to handle it.  Zephyr, if you take a step back and look at him, is antithetical to every other chuunige protagonist in existence.  The cynicism isn't a problem.  Roughly half of all chuunige protagonists are cynical on one level or another.  The pessimism, while extreme, is nothing unusual.  No, what makes him unique is his sheer... baseness.  Zephyr, at his core, is a weak man who is perfectly willing to stain his hands with the blood of the innocent and the good to protect what he cares about... in order to protect himself.  Zephyr is a coward, he is not only afraid all the time in battle, but his first impulse is to run away whenever a situation gets hard (though that fleeing takes different forms depending on the situation).  When he is confronted with someone who sees him an obstacle to their ideals, he wants nothing more than to trample and spit on the glory of the person in front of him.  Zephyr is essentially the embodiment of the part of us that is envious and resentful of those more capable than ourselves, with his only saving grace being that he nonetheless can at times drive himself to stand against his own nature. 

In other words, in 99% of all the games I've played, he'd essentially be one of those petty minor bosses who got squished like a bug by my level 10 characters.  He is also very similar to Rusalka from Dies Irae (if you have played the game, note her Creation spell's essential meaning). 

Zephyr is accompanied by Vendetta, an artificially weaponized and resurrected corpse with an unknown purpose who is psychically linked with him, who constantly kicks him in the ass to get him to be a man and be a better person (which is often hilarious in and of itself, since Zephyr has no intention of doing so on his own). 

On the other side is Christopher Valzeride, an undoubted hero who gives selflessly of himself, who never gives up, who moves forward with no desire for recompense.  In most chuunige VNs, Valzeride would be the protagonist.  His intensity of spirit, his iron will, his burning idealism... combined with a realistic understanding of the costs of his path forwar... make him an ideal archetype for a chuunige protagonist in a 'heroic style' chuunige. 

However, the fundamental theme that starts out the game and resonates throughout all the paths is 'What is victory?'  Zephyr is a man who has been destroyed, carved away, piece by bloody piece, by his own victories, gaining nothing but more pain and the next, even more difficult battle from anything he achieved.  He is the picture of a man forced into a role by his talents and utterly unsuited to it by his essential nature.  Valzeride is a man who seeks victory above all else and merely accepts the greater tribulations that await him as the price of his path. 

Essentially, the two men are polar extremes of human potential that encompass both the best and worst of the two extremes.  Zephyr, while capable of kindness and gentleness, is cruel in his cowardice and malicious toward those who corner him with their valor and vivid idealism.  Valzeride loves human virtue but is utterly incapable of kindness or personal empathy, as his own nature rejects anything ambiguous and weak.  He honestly can't empathize with the suffering others draw from their tribulations, and this is why he serves as a great antagonist, despite essentially being a truly virtuous man in addition to being a hero.

Silverio Trinity

Silverio Trinity focuses a lot more intensely on the nature of the 'Light', as embodied by Valzeride in the previous game.  It portrays those who take after him as 'Zombies of Light', men and women who simply move forward because they are incapable of conceiving of any other course of action.  As is said repeatedly in both games in various fashions, 'A hero of light continues forward, running over the hapless individuals who get in their way, unable to compromise, unable to consider the suffering of others except as the price for the brilliant shining future they seek to bring about.' 

Ashe, the protagonist, is by nature a good and caring young man.  He can be driven to anger for the sake of others, and he has a deep well of compassion that is honest in its depth... and contrasts starkly with the other characters aspected of Light, such as Gilbert, Helios, and even Dainsleif.  Ashe recognizes and empathizes with the weakness of others, and his understanding of them is more than just the intellectual recognition you see out of individuals like Valzeride and Gilbert.  In this fashion, Trinity is more of a contrasting of common humanity with the two extremes of human nature (darkness and light as represented by the protagonists and antagonists of Vendetta).  Its narrative, while having a different locale and characters, is a direct continuation of the conversation with the reader begun with Vendetta, and its conclusion is interesting, to say the least (Edit: Though it can be said to be a typical conclusion for such 'conversation' in a Japanese VN).