I've noticed a few problems and troublesome quirks with this mod since I've been using it.
In one of my playthroughs with this mod active, I decided to check out how it works when you side with the templars, which as I understand it (and only know about because of a comment in this thread), is only possible by just mass killing non-pirate, non-templar fleets in a system during an active crusade. I had 100% cooperative standing with every faction except pirates before starting to contribute to the crusades, at which point I started killing only independent fleets within crusaded systems. Doing this enough seems to raise the Templar's opinion of you after the crusade ends, and lowers your faction standing with every faction present in that sector, even if you've only been fighting one of them.
Now, this could be a problem if for some unrelated reason you are just already fighting one of the non-pirate factions, and happen to fight them a bit during a crusade, especially one where few or no templars actually show up during the entire event, so you might not even notice, or forget between play sessions, though it's not at all impossible to recover your faction standing from contributing to a crusade just once. In this way, it is at least possible to only be permanently hostile to one non-pirate faction, and just fix your losses with with everyone else, and make it to cooperative level with the templars. It takes an extra long time and a lot of concentrated effort, though.
Another thing I noticed is that once you do gain access to the templar's home base, way off in the middle of nowhere, far removed from the other systems, you don't even get the option to purchase a place to store ships and weapons, even after reaching max faction standing with the templars.
This is problematic not just due to the distance from everywhere else (especially combined with the fuel and extra high supply costs of the templar ships), but also for the fact that under normal circumstances, a player allied with the templars will have made permanent enemies with most or all of the other factions by doing so, and thus be unable to dock and store things anywhere else except the abandoned platform in Corvus, and completely unable to resupply and refuel other than by fighting huge enemy fleets, which is not enough to support the extra high maintenance supply costs of templar ships, much less the fuel costs of getting from system to system without having to slog all the way back to the templar home base, where you can't even store anything extra.
It also seems like the templar home base should have at least one of every one of their ships and weapons available for purchase in the market at every new market update cycle, since you can't very well just store all your ships and crew right there at the home base and just wait around for months and months and months at a time with 0.0 supply cost, hoping for the RNG to produce the number and kind of ships you require, and traveling the enormous distance from a populated system all the way back to the templar system and base is both boring and time/resource consuming to an extreme if you have more than a frigate in your fleet (which is impractical when all other factions are hostile to you), and yields desired results even less often than just waiting around the templar base in fast forward mode for hours and hours. Hours and hours of real time, that is, after which I still never saw a templar carrier or a joyeuse cannon, after speeding through ingame time on a scale of years.
The amount of effort and the sacrifices that have to be made to fully ally with the templars seems right, but basically, if you've worked your way to cooperative with the templars, they should at least be more minimally accomodating to a player that they consider their invaluable comrade, I'd think.
On a side note, it'd also be nice if the templars had a few or a lot of patrols all around the universe that were quite a bit smaller, like just one or two destroyers/frigates, and saved the really huge fleets mostly for crusades. At the moment it mostly seems like an all-or-nothing affair to fight them that first time, where if you turn them hostile before you have 40+ levels worth of perks and a fully decked out paragon or two, a massive fleet is going to easily run you down, or catch you by surprise and easily destroy you with vastly superior power AND numbers. Even if your fleet is a few big and powerful ships, you're not ever going to win against half a dozen templar frigates/destroyers, which can also always catch up to you.
Great mod though, still enjoying the shiny effects and overwhelming opposition immensely.