Hello there!
First of all, I enjoy this mod troughoutly, but I have a few ideas/suggestions how to make it better.

First of all, the Enclave misses the Basic Power Armour tech wich is not much of a big deal since you start with APA,
but you miss out on +5% Breakthrough and Soft attack by the end game, and it can be felt.

The case of new reno.
It has a route to become the enclave.
If that happens it would be nice if the enclave would annex the territory instead of being two enclaves.
Although it would also serve as a hinderence for the Enlave in the short turn.
As New Reno completes focuses related to the enclave, it could have a short time adverse effect/gamble for the enclave.
When the Calling in Old Allies focus finishes, you are asked if you send in the manpower or not.
If you do, you will lose 200 Power Armour and Infantry equipment,
not to mention 200 manpower which is a lot in the beggining of the game.
This would also mean Dronan would leave here, and would be unavailable as an advisor until his return.
Sgt.Granite's Defence Company would be especially devastating on a Reformer Playtrough,
because it would cause the loss of technocracy, which already comes hard with all the Purists around.
On the purist route, it would replace the current Granite Defects event with a loss of equipment as an added debuff,
but it would mean Granite returns after the reannexation and it would mean a higher number of support for technocracy after his return, since he hand delivered New Reno.
The Enclave Technician focus, it would grant you the "Technicians away" national spirit,
which would grant you production debuffs to infantry equipment equal to the bonus New Reno gets.


About specific branches:

Let me start off with the Purist branch.
The Clearing out the Natives branch does not bypass if you already control the territory,
and this is the only one of the focuses on this path, so I believe this is a mistake, but I might as well let it be known here.
The Reclaim Navarro focus could give a core for the Enclave.
That 1.5K manpower you get in the state wouldn't be gamebreaking but it would give some place to expand to quickly and would help you out a bit.
Also the Purist Branch is generally lacking compared to the Reform Branch, but is way too powerful.
Either way, the whole branch should be nerfed a bit.
More events that bring up the NCR's suspicion should occur so expanding would be riskier,
since the Lawless Wasteland does not cound towards the state modifier of the NCR Suspicion, only the one time they were conquered.
The easiest solution I see would be that any time a nation goes "silent", the NCR becomes more and more suspicious.

Now for the bigger problem...
Since they don't use the cap system, they are unable to upgrade their spy agency. The ageny can be created no problem, but each upgrade costs caps.
This lead to the situation that you can't have multiple agents and even that agent is worse than the agents others have access to.
I understand the reason behind them not having caps is the fact that they shouldn't work with anyone, but this sadly locks the intel agency out.
Possible solution would be to maybe give them access to agency upgrades trough decisions.


Reformer path:

Nevada Branch:
Securing the Big MT and Restoring the Big MT should have the condition for you to own and control the state, as you can complete them while the Desert Rangers have the state.
And since the Restoring the Big MT focus gives out building slot and factory as a bonus, as soon as you conquer or annex the rangers you instantly loose both.
The State of Utah focus is very flawed at the moment. If New Canaan is in a faction, it does not leave it and becomes part of yours,
and if I manually remove the Mormon alliance using even cheats, they just leave after a short time. I think the reason is the fact that they are a different ideology.(either people or elites.)
An easy solution in my opinion would be to add a modifier that the states that join the union can not leave it or make them be ruled by intellectuals as well if they join in.
The bone dancers usually conquer Chemult Station by the time I have time to do so, since I am working on making friends with the NCR,
(since I can't have a lot of states if I don't want to be wiped out by them), and if I conquer the bone Dancers, I can not give the bone dancer states over to the pacific northwest.
I think I could release the bone dancers/crimson accolytes, but then I would loose all my cores on Chemult Station as well, which I do not want.
A similar decision like the ones with Deseret where all of the states give up the territory they have of the northwestern commonwelth would be an easy solution.

And here comes my greatest new idea implementation of the whole rant: A tech sharing initiative withing the Reunited States. Nevada would be able to share the unique techs with each of the states.
It would really go with the we are stronger together mentality of this route. It's not about conquest, but reunification.
It would couse a loss of either stability or war support depending on what you share, but having the option to give the NCR the APA and the Vertibirds would feel organic.
Even more so when the NCR AI would do a decision where they give you the(for example) General Atomics schematics which they found with their scavengers.


Restoring a Nation Branch:
The Cleansing the Mojave focus does not autocomplete if you already control the Mojave/the mojave Chapter is dead. It is weird to have a wargoal stuck with me after the target is long dead.
The Stripping the Vaults focus does not work? I think?
I never got any Vault related decisions.