The thing you have to keep in mind is, what type of faction you want to do. If it's a NPC faction, you are pretty much free from any limitation as long as they aren't boring/too strong/too weak to fight against. If it's a player faction (which I suspect) you must favor player agency.
One of the core and novel mechanic of Starsector's combat is the managing of your flux that govern your offense and defense. This offers a lot of tactical decision making in combat and in fitting your ship (although this has been considerably reduced by the recent missiles buffs since venting is now as much a death sentence as overloading). To tank a hit on the shield or hull require quick reflexes, a good knowledge of the universe to assess the threat, a good knowledge of your ship's characteristics, and commit to either action. That's what make the game so exiting, rewarding for the veterans players, and surprisingly deep in gameplay.
The second very interesting mechanic of Starsector is the ship system. Those allow to enhance your ship's performance or give you an edge and must be used wisely (again, player agency). You have to refrain from spamming them and wait for the right moment to make the most of them. You'll also notice that , with very few exceptions beyond civilian hulls, ships that don't rely heavily on their shields have a ship system that require a lot more commitment, to compensate for the lack of finesse involved in managing their shield. You don't burn drive blindly in an enemy fleet!
Finally there is the ship customization load-out mechanic. It may not look flashy, but that is a very important one to make the most out of the other mechanics. You can optimize your ships to your play-style, compensate for the hull weaknesses or on the contrary stack on their strengths... And with skill opening more options, it reinforce the sense of character progression. You may have noticed the sharp difficulty difference between vanilla and SS+, and the largest part of this spike comes from the random load-outs the AI have: Vanilla load-outs are voluntarily non optimized and facing an AI on a mostly even ground (the player still has the benefits of the fleet wide bonuses) is a nasty surprise the first few times, until you adjust your strategy. This show how important thinking about your choice of weapons is.
Now removing to a large extend those mechanics is a huge deal, it will only leave the tactical aspect of the game to positioning, and since we are talking about large ships that doesn't mean much: a shield-less, system-less, hulking faction will only be able to sit in range, all weapons on autofire and duking it out until the ship with the less HP will die first. Not the most exiting thing compared to the vanilla gameplay all about split second decisions and preparation in refit. It will certainly have a certain appeal at first, if only for the nostalgia kick. But that might be short lived, or people might only keep them as a NPC faction and for the occasional weapon they drop. You are about to invest a lot of work in this if you want to bring it to a good level of polish, and such outcome could be disappointing.
The core gameplay mechanics of Freespace are based on the piloting of fighters, you can't port that into Starsector, and their large ships aren't sophisticated enough because the game was all about fighters.
I would advise you to rethink how much you want to respect the original Freespace franchise. What are the core principles of Freespace you want to bring in Starsector? If it mostly concern ships sprites, tons of fighters, and huge slashing beams, your mod wouldn't be worse from using the same mechanics as vanilla: would it be so bad if all ships had shields instead of just the fighters? Systems are often difficult to design, but they offers a lot of way to add some flavor to a ship design and to the way it is played. Adding those wouldn't suddenly break their Freespace heritage...
If you are set on using shield-less ships, you'll have to think about something to replace that: Templars have the Priwen Burst, Exi have their temporary Repulsor, some blackrock ships have their Scalar-something-bullet-eating-lightning-spewing mechanic... All these ships replaced the shields with something else as to maintain the amount player's agency available when flying them. If you don't have that, you better have at the very least an awesome ship-system.
I'm not a fan of IP mods specifically in Starsector because usually they try to stick too close to their source material and remove everything that make the game worth playing in my opinion. If they were only keeping a loose relation, they could take the best of both worlds and be very much worth playing. But that's only my opinion, so feel free to ignore it if you disagree. In any case, good luck with your mod.