This discussion is absolutely fantastic, and it brings up a lot of "issues" I personally had/have with JTL given growing up with the X-Wing Vs. TIE Fighter series, and especially X-Wing Alliance, along with all of the Rogue Squadron games.
I was a kid when I played this back on live, so I hadn't the slightest clue about what worked and what didn't, I was just completely and totally enamored by the customization that JTL allowed for. Being able to have different engines and weapons along with paints and textures on my ships was *mindblowing* to me at the time, and it still is. Moreso now that nothing even remotely attempted something similar to those games since. (I don't really count Star Wars Squadrons, as it was effectively a gutted X-Wing Alliance with an absurd focus on PvP that just looked like a half-baked 4KHD Unreal Engine 5 demo parody you'd see on YouTube.)
Speaking of, the XWA Upgrade Mod is PHENOMENAL if you ever get a chance to try it out. I wish we could spruce up the space game here with some of their tweaks, models, and knowhow, because having their work in a game like this that is so open to player freedom would take it to an entirely different level. Though, I digress.
Getting to the main points about balance, I have to largely agree on a lot of the ships mentioned. There is quite literally no statistical difference between the TIE Interceptor and the TIE Advanced outside of its mass, weapon slot count, and hitbox. The A-Wing, despite supposedly being the TIE/A's mirror is objectively worse in every single stat; the only equal stat is its mass cap. The TIE Interceptor is also a Tier 3 ship, making it completely redundant vs. the Advanced.
You are correct on that some Imperial ships were not installed with shields, however that was only a major issue for TIE/f series craft, and was an optional upgrade on Interceptors and others. Largely due to the immense expectations the Empire had on its pilots.
The TIE/In(terceptor) has 4 hardpoints, yet 1 weapon slot. The X-Wing has 4 (6 for Advanced if we really want to let it be special, haha) hardpoints, and 2 (3) weapon slots, and the B-Wing is the only one with 4 hardpoints and 4 weapon slots. The strangest thing is that you can't change the linking of these cannons in any real way outside of the weapon slots, so the only workaround would be to make a weapon slot for every hardpoint, which could lead to some mass issues very fast if they aren't adjusted appropriately. However, that would likely mean a *lot* of re-crafting of chassis which may or may not upset shipwrights.
There would definitely need to be a lot of rethinking of how you would appropriately progress these in the piloting trees as well too, because according to the lore, the A-Wing was one of the hardest ships to use, yet it's granted certification very early on. There are some redundancies that need to be addressed too, as I'll mention below.
There also a number of issues plaguing the piloting skills that need to be looked at again to make... practically all of them not only more desireable to use, but also more evenly balanced across the piloting profession, although I'm still drafting up a solution to that problem among other things. I am in agreement that JTL could use a little more "X-Wing Alliance" in its mix to really make space far more fun and engaging, because outside of a couple of things once you've finished your Ace(s) there's not really much else to do outside of Destroy duties, Space GCW Battles, or Piracy Convoys.
If anything, I was thinking about a lot of what has been discussed here already, and it's nice to see out in the open that I'm not the only one that feels this way. I don't believe player ships should be so held down by lore that they're stripped of shielding or even super overpowered that nothing can stand a chance (looking at the TIE/D). One possibility if we did go that way would be to increase chassis armour and HP of Imperial craft to compensate for lack of shielding, but you cannot shunt, reinforce, recharge, or repair armour/hull mid-flight. Stopping at a station to repair every so often isn't the most practical ask either. Nor would it be respectful to all the currently crafted chassis out there if it wasn't made into a retroactive change, which I don't think can be done with crafted chassis. Don't quote me on that, though.
The TIE Bomber should not be that late into the Imperial career either, I agree. I also believe the Y-Wings need to be entirely revisited. Lore-wise they're different models (The turreted version is the BTL-S3, the Longprobe is the BTL-A4), but the only major differences in-game are mass and... the fact that the Tier 3 Longprobe ship doesn't need a gunner to use the 2nd weapon. I would've expected them to be granted the other way around, given the fact that the TIE Aggressor is granted so late, and the Dunelizard is effectively the Neutral's Y-Wing as their 2nd ship.
I also agree that more of the iconic ships we know from X-Wing Alliance and games of old should be represented in JTL in some format. There's a lot that needs to be adjusted and reworked, but I think it's doable even if it may take a bit of time. Those games were my childhood, and after experiencing some frantic space battles even within JTL with some group quests, I can safely say that this game needs more of *that*. I think the game in its current state plays space a bit too safely, if you understand what I mean.
Though for the record, I am not on board with the idea of simply making higher difficulty enemies have more HP/Armour and hit harder. I feel that that kind of method of adding difficulty is a very lazy and uninteresting way of approaching it, and doesn't really test player skill or push for improvement in any meaningful way than just "lol just don't get hit as much." When you consider the NPCs success rate in hitting you is a blend of chance and physics rather than actually... y'know, physics entirely. At least that's the way I understand it.
In any case, glad to see this.