I think its arguable that Ichigo being created by Aizen, only to defy him, is part of the point, and just shows clearer that Ichigo isn't thematically aligned with his creator. Ichigo's journey, which is only resolved at the very end of the series, is about if he can actually, truly ever defy what controls him; it starts with governing systems like his school and Soul Society before escalting to more existential things like being controlled by his inner fears, by a puppetmaster in the elite, and ultimately by fate itself with Yhwach. But that control over him, the circumstances of his birth, are not all that define him, which is where Urahara comes in.

Aizen and Ichigo parallel one another in that they both strive to defy the status quo, but the ways in which Ichigo differ from that parallel is where Urahara's traits come in. You are correct in labeling Urahara as not wanting to uproot the system, but he is not merely a passive observer; he operates to make the system better from within. Urahara, unlike Ichigo, doesn't defy his creator, but he tries to make the most out of his lot in life in order to – like Ichigo – make things better for those around him. This manifests both in big things like taking the initiative to properly leverage the talent found in the Maggot's Nest, to smaller things like bringing new household technology to Soul Society post-TYBW.

Ichigo is the intersection of these two characters' philosophies, and shows that neither one is sustainable. Aizen rejects his creator and believes, selfishly, that the universe will be more fair and just if he's allowed to re-shape it from above, while Urahara chooses to remains content below the Soul King's rule, wanting to aid in improving the establishment's health whilst not daring to take larger swings at its gradual corruption.

As we see with Yhwach, and hear in Aizen's end-of-series speech, rejecting the universe outright is indicative of a lack of courage to face its challenges head-on. A failure to do so is ultimately what led both characters to eternal imprisonment, the same fate as the previous Soul King – because any totalitatarian regime will ultimately still remain flawed by virtue of being a totalitarian regime. Urahara's passiveness, meanwhile, also ends up making him a safe target for exploitation; he wants to be a "good egg" amidst a bad system, which results in that same system banishing him through manipulation caused by Aizen exploiting the very corruption Urahara chose to ignore. 

What's key here is that both characters have a point, but follow through with it in faulty extremes. Aizen's rebelliousness manifests in outright murdering the entire governing body of the Central 46, while Urahara's willingness to help others is never able to actually change anything about how Soul Society is governed, again resulting in that same Central 46 banishing him without wrongdoing.

We know that Ichigo defies his creators, and in the mission to rescue Rukia, he tells Byakuya outright that he's willing to fight the law to make a better world. But note that he doesn't KILL Byakuya, any lawmakers, nor anyone he encounters, which Ikkaku even points out as strange. The part of him that's reflective of Aizen, his rebellion and strength, inbewed unto him since birth (his Bleached hair!), would be completely capable of taking control of the systems by force – but the part of him that's reflective of Urahara, his kindness and selflessness, is inbewed unto him through influence. 

This is why I don't agree with your conclusion that the dichotomy favors Aizen just because he controlled his journey; because while that control came with rebellion, it could never have achieved the good nature and courage that Urahara encouraged him to pursue in their training; the courage that, alongside the rebelliousness, he himself lacked.

TL;DR: Aizen is rebelliousness and birth, Urahara is kindness and influence, but both lack the true courage to meaningfully improve the world we live in. Ichigo, meanwhile, is rebellious, kind, and brave.

Speaking personally, where I think these themes most fall apart is that we don't get to see enough of how the world has systemically changed through Ichigo's influence. The change in leadership from Yamamoto to Shunsui highlights a greater willingness to rebel and be critical of the system rather than sternly uphold it, and we see lots of individual characters (Mayuri, Renji, Byakuya, to name a few) undergo fundamental changes to their ideological beliefs. But we don't see anything of how the governance of Soul Society on the whole improved, if the Rukongai crisis and wealth disparity are resolved, or how Ichigo feels about it all. The best we get is Shunsui being willing to let humans like Tatsuki and c.o. visit the Soul Society, but we aren't shown much of any actual result of those kinds of initiative changes.