Novgorod was so focused on itself it had troubles controlling Pskov (a place they regarded as a daughter city and a fellow republican state), and the freemen of Hlynov hardly ever paid Novgorod any taxes or send any representatives despite being all from there originally.
Here's a list of problems with Novogord vs. Vladimir:
1. No standing army, combined with elected generals. Leads to a lot of military losses, though I suppose that could be changed. Coupled with a lower land productivity and lower population than Zalesye, and you can see how the long term looks bad.
2. The vast Novgorodian territory was controlled directly and in a hereditary manner by the Great Families like those of Borok (Boretsky); Novgorod was trying out feudalism when Moscow and Ryazan were moving towards Ottoman-style Service Gentry. Guess who could raise more professional soldiers that wouldn't be anxious to hurry back for the next election?
3. Moscow (and to a lesser extent Tver, Ryazan and Lithuania) actively recruited talent. Moscow's noble houses come from Crimea, Circassia, Lithuania, Kazan, the Great Horde, Prussia, Wallachia, Poland...you name it. And of course Novgorod. Anyone could serve the Grand Prince/Tsar and provided they had some ability would quickly achieve prominence.
In a republican system like Novgorod's, the Grand Prince/Tsar wouldn't be promoting you. You had to promote yourself. And if you wanted estates, you had to start machinations to oust some of the current owners out.
Needless to say, service gentry provided the professional fighting force. See point #1.
4. Moscow, Tver, Galich and Suzdal all fought over Vladimir. Not only because it's the biggest town and it's on the biggest fertile plain in Zalesye, and not only because it's the historical capital, but because it has the Metropolitan.
That is a HUGE factor. It had the spiritual leader of all Russia what was widely recognised as such in an age where it really mattered. He was the one endorsed by the Patriarch in Constantinople.
By contrast, the position of the Galician-Lithuanian orthodox Metropolitan was used in a very cynical manner by the Lithuanian state, and things only became worse once Lithuania took on Catholicism.
As for Novgorod - their elected Vladyko, the Archbishop? Wasn't a recognized archbishop. As far as Constantinople was concerned Novgorod only had a bishops's seat.
So when Moscow wins the struggle over the legacy of Vladimir, they have the legitimate Metropolitan (later Patriarch), and Novgorod has a local, elected prince-bishop. Which is more useful for the unification?
5. Novgorod's North had its primary value in the ability to gather fur tribute from the locals, whether through the Finnic/Russified nobles or through the managers of the great boyar estates.
Except that as early as say 129x, you have unregistered settlers from Zalesye coming north to escape the Mongol raiding and settling everywhere. Good you say? More tax base? NO, bad.
They did not recognize Novgorod's rule! They often fought with the old Russian settlers and local Finns alike. They fished, farmed, and paid no taxes. And if the Novgorodian boyars tried to force them they...appealed to their nominal sovreigns. Typically the princes of Galich-Mersky.
Who of course couldn't collect taxes from them either but were more than happy to raid Novgorod's domains and grab that fur tax for themselves. And Novgorod's republican state was never quick enough to react.
Already by the 1320s you have various Zalesye princes traversing Novgorodian lands to go and gather tribute from the lords of Pechora and Yugra, who were supposedly Novgorodian tributaries since the 11th c.!
...with relative impunity.
6. Novgorod had a terrible notion of what diplomacy looks like. Because of their elected offices, they sent hotheads where tactful folks might do, and frightened men to places where one might need some inner steel. Other than with Lithuania and partly the Hanse, they never managed to establish a single lasting alliance.
They even gave away two strong claims over their entire state to Moscow, based on the language of the diplomatic protocol which the envoys misused, and which Moscow later pressed for.
7. Novgorod's rash young men (of the same kind that once founded Hlynov) often banded together to go for ushkui raids that hit Russian and Tatar cities down the Volga, sometimes pretty seriously. They (or their vassals) were also engaged in serious raiding/counter-raiding of the same kind with the Finns who were under Swedish sovereignty.
They were basically latter-day Vikings, as late as the 15th c. River pirates that the state tacitly supported. And they often attacked the very areas from where they could otherwise import grain (Kazan! Russian princes extracted so much bread from old Bulgar it boggles the mind that the trade never resumed after the Horde weakened).
Nobody likes pirates.
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I mean, I really do like Novgorod, and I almost wish Russia had a longer "Italian" period where there were republics and city-states that competed and tried out new things, but I hope I explained the internal challenges well enough. They'd have to be addressed before one can create a Novgorodian Russia.