I know, there are two different charges allready, one that deals increased damage and one that increases the speed.
But thats not what i mean, lets start:
While leveling my Guard, i noticed that i always laugh about LFRs.
I can just switch my shield to Thermal and they turn completely useless with the module.
If they start shooting me with the main weapon, i can switch again, they can only do one thing at a time.
With my Jericho LFR i noticed then very soon, that i stopped shooting Guards with my Missiles.
I totally love Jericho LFR and hope that they will get the “secret project” of them along with the other ships that may come in…atleast i heard that they want to implement the missing ships, so i hope that they implement both LFRs and not just one.
Using the Missiles to damage some interceptors or even kill them at long range is just nice, supporting my team from behind the lines is also great.
But the limitation to Thermal is a little bit…meh
So thats what the suggestion is about:
Two New Modules
Base effect:
The Modules will work like the “aura modules”, switch them on and they stay on, not just for one shot.
While they are active, your LFR Sniper/Missile will change to another Damage Type - EM or Kinetic (turning them off switches back to Thermal)
For Jericho this would also change the Cloud then.
Those modules would give your Sniper some additional use.
As far as i know most shields are weak against EM, while hull is weak against kinetic.
So if you see a guard with full shield, switch to EM to drain a good amount of his shield.
Switch to Kinetic to deal a good amount of damage against unshielded targets.
Or just use thermal to work against both until you find an enemy who ignores thermal damage…
Changing the “Ammo” would cause a Module cooldown of like 10s (imagine it as reloading)
Secondary Effect
Those additional effects would change the LFR Special even further, from pure long range damage support into a better long range Team support role
Since just changing the damage type might be usefull sometimes, it would not be worth it to sacrifice a slot for it.
So i thought about adding secondary effects to them.
Thermal would still be the usual “decent agains everything” type while Kinetic and EM will have a different role that is not based on pure damage alone.
Since the Missile and the Disintegrator work so different, it would be hard to find one mechanic that fits them both - so we would need two.
also it would benefit your team, so that you are not just the “killstealing camper”.
The two different effects could be:
Empire:
Since the Sniper is called Disintegrator in Thermal, why not thinking that further?
EM would be a Disruptor then. Disrupt the shield of the target, reducing the Shield regeneration (including the regeneration caused by certain Modules), works only if the projectile hits the Shield.
Leveling increases the strength and duration of that effect
Kinetic would be a Nanite Charge (yes i know, Engineers Nanite-Gun thingy deals EM…but whatever) , reducing the Hull resistance a little bit.
Works only if the projectile hits the Hull.
Leveling increases the strength and duration of that effect
Jericho:
Its a Rocket, its different from the Sniper since it Explodes and creates a Cloud.
As allready mentioned, the cloud would also change its element.
Actually…that one is a bit harder to think about, so i thought that the “Charges” will change the damage type of the explosion and the type of cloud they leave.
EM creates an EMP flash when exploding, removing locked targets for enemies in its range (not like a time based effect that the other LFR module has, dont know what it is called)
While inside the cloud, targets cant lock on anymore. Also it adds some visual interference.
Leveling increases the range of the blast and cloud
Kinetic creates a Shrapnell Cloud that jams enemies engine. This cloud deals damage based on the speed of the ship that flies through. So standing still or just floating through without the use of the engine would deal no damage.
The amount of damage could be 10x the speed you move through. So a slow frigate with around 200 speed would take 2000 damage per second, while a fast interceptor at capped speed with 700 would take 7000 per second.
Those number are just to show how the effect would work, dont worry 
Cloud becomes active a short time after the detonation to give fast fighters a chance to not die instantly when you hit them directly, so they can react to it by releasing the acceleration key and float through the cloud as it forms.
Remember: just stopping to press the acceleration button negates that effect, since you would not use the engine and just float through it.
Leveling increases the duration of that cloud
Needed Faction Tokens
Kinetic Jericho (since they allready have all the other kinetic stuff too)
EM would be Empire
Summary
Pro:
Changing Element to increase damage against certain resistance types
Better Team Support besides pure long range damage
Con:
Less damage against the other mitigation type (EM deals more against shield but less against hull, Kinetic the other way around)
Uses a module slot each
Against Guardians, you would benefit from having atleast one of the Damage-Type changes equipped.
For Empire, Thermal would still have the advantage of dealing similar damage to shield and health.
EM would help your team against shield tanks
Kinetic would help against hull tanks.
For Jericho, Thermal would still be the usual damage cloud for some additional damage.
EM would help your team for example against slow long ranged projectile-users, since they could not lock your team inside that cloud.
Kinetic would help your team against fast enemies or to stop enemy movement inside the cloud