I think it's a non issue. Whatever you do you'll always end up with a rock paper scissor system which is also realistic in the weapons world.
For the rest you have to Role play it otherwise as things are you always use Gauss as PD for instance.
I think the only way through it is to accentuate more than it currently is (and there is much) the difference in tech not only by kind but considering the level.
You may have very powerful and convenient Rails Guns but after the level 5 Lasers Would be much better etc, but as said that is already there and honestly, as Jorgen already said, unless Steve decides to change the whole mechanic I don't see any light at the end of this tunnel and I would leave it as it is.
1. Railguns right now are really neither rock, paper or scissors, its more like curiosity or as you said, roleplay anchor
2. Roleplaying alone, imagine lying to yourself to use bad cards because of lore. Roleplaying perspective is nice but makes for a very, very bad argument (amd and i am speaking from game developer perspective as well), to discuss anything. If you really want to role-play, lets say your race needs to play while literally sitting on hard, pointy rocks, and so do you, or for example you need to play on single 480p glitchy monitor because, again, reasons. Its one thing to tell a lore (i.e. excuse for the current, already existing, events) and excusing non-written lore based on whatever you are stuck with (broken monitor, sitting on rocks, bad mechanics). This may interest you, but it also may be only you. And for my own sake i would like to parody this point later (marked "ROLEPLAY" all caps). Also if you want to be bullied, you can enjoy it with any mechanics presented, there is no need to any balance the game specially for you.
3a. difference in tech, yeah, as i wrote in 3b, but scaled vertically, however tech costs the same across levels so keep it in mind. smegty lvl(N) gauss costs around the same as lvl(N) lasers, while both performance and flexibility are far, far, faaaaar off each other.
3b. balance - despite how lore and universe and all the other stuff presents itself, there is no reason to make mechanics more exciting and flexible for the players. Consider this, lets have all of the weapon technologies researched to, lets say, around lvl (N), what your fleet can do to be on par with anyone else:
- gauss - ok, since there are no torpedos (i.e. high yeld, possibly armored, in some cases swarmed projectiles) anymore, you need just 1 point of damage to kill a rocket, so gauss is a cheap option here, for anything else? too big for FAC, questionable for bigger parasites... May work for STO not really goto path for larger ships, unless you ROLEPLAY then every piece of ... can be your weapon. Also i just checked - i can install 3 1-size box launchers for the const of 1 8%-hit chance gauss (smirk)
- railguns - similar to gauss, since those work on similar research trees, medicore for AM turrets, can do some corvettes (not FAC, rather up to 2K ton, possibly parasites?) if you desperate or ROLEPLAY
- microwaves - blind/wound only, useless for mostly in bigger fights against anything really. You are encountering a huge fleet and there is really no incentive to get closer. If you would like to go for the "blind and kill" tactic on smaller fleets, that's nice and may work. You may be even able to board some ships if fleets are small enough, but this is highly specialized path to go. You can do some fuc...ery, like capturing enemy transports, and i think this is not a bad thing to have around, especially that there is no alternatives, but range is not really top notch. Although it adds to range of available weapons/mechanics and flexibility.2
- lasers - go to weapon. If someone wants beam ship, lasers are literally the goto technology. Distance is mostly limited by BFC rather than laser performance, and i successfully used them to sow mayhem, even to large fleets. Also due to good range works great for PD since thise can shoot multiple times before close-in. There is no good reason to opt for anything else, especially that damage pattern is better than on anything else. FAC is limited since it cost at least 200 tons to put smallest laser onboard, but still...
- particle beam/lance - kinda sniping weapons, but not really, just big lasers IMO, not really replacements for missiles, quite light for given performance. If you want to have beam ships, and you are able, you are opting for this. Nice range, nice damage, nice pattern. If you are able to one-hit something, you are using this nothing else. Especially if there is up to 4-5 armor layers. If you are not able to pierce in one shot you either run or designated another target since there is not really a point in repetition with this gun. Plays really nicely with fleet composition. Even more OP than lasers considering beam weapons only.
- mesons - nice thing on high level, but since it now scales with armor its kinda balanced wit the lasers. Superior range, but you cant use it either way since you are blocked by the BFC again. Can do damage in the same way particle lance does, but with particle lance you do not gamble. May be good for corvettes/swams (i guess kinda too big for FAC, but by corvette i mean something up to 2K ton, optionally with a turret). If i would need to choose i would go for Lances. It WAS a good weapon against armored torpedoes but since those do not have armor anymore, smallest laser is good enough if not better.
- coronade - never used those. I mean, yeah, damage and all, but you will loose precious [fleet+fuel+maitenance] with each attack or at least wound your fleet, since most of mid-tier PD can hit you in this range. As earlier said, fun for ROLEPLAY but not really useful IRL.
so summarizing:
- there is around 2 choices if you want big guns/sto, (laser or particle, mostly the same)
- there is 2 choices if you want PD (gauss or laser?)
- there is 2 choices good for fleet composition/situational fights (meson,mv)
... so where are the railguns? of around 7 beam weapons available so you are going to go for lasers/lance (only beam weapons) if you want performance, on some occasions, m.a.y.b.e (mesons/microwaves) for fleet composition or situational fights, anything else if you want ROLEPLAY or punish yourself. This is the proposition to make railguns (also means railgun tech tree) more viable and also introduce new mechanic alongside.
And now, do you really think that there is no room for improvement here? Again, railguns and gauss are really copy-paste boring mechanics. There is still afield for improvements since current weapon collection gives a lot of room to work with.
I gave initial proposal of the weapon and balancing, considering both smaller and larger ships. Mechanic could work well with fleet composition and logistics of the fleet. The reset depends on choosing the right featues, proper balancing/adjustments to the mechanic, community's approval and Steven's good will...
...ROLEPLAY(smirk)....