How do you think this game would change if there was a weapon with the following characteristics.
The dematerializer.
Range: extreme. (3000-5000)
RoF: 200
Tracking speed: 0.05 (essentially, can’t hit moving targets)
Damage: 2^(number of previous hits). So it does nothing at first but after four or five seconds, it simply disintegrates anything.
I assume this is your weapon to deal with engineless ships. 
First off, I’m not sure if it would work, since tracking speed/target speed isn’t the whole equation - there’s also size in there. If I remember right, anything below 256m long has a chance to be missed even when standing still. So, the weapon might not hit even a stationary target reliably enough to build up the string of consecutive hits required for severe damage.
Speaking of which, I assume you’re suggesting the damage is based on number of previous consecutive hits, not just hits, period? Otherwise a string of lucky hits on a moving target could doom it.
But most importantly, if it works as intended against engineless ships, it will also annihilate perfectly mobile ships that just happen to be holding still for a while (e.g. missile ships that have reached attack range).
Finally, I don’t think it’s desirable to put a mechanic in the game that makes fielding immobile ships total suicide - at that point you might as well just require engines on everything instead. If immobile ships are going to be an interesting part of the game, it can’t be as simple as “well, I hope they don’t have x weapon along!” A choice with only one good option isn’t a real choice, after all.
I think I’m with Supraluminal on this one. Essentially, this punishes any ship which is immobile, very slow, or sitting still for whatever reason.
If it’s trying to address the fact that many people are making fleets of immobile ships, I think there’s a better way to do it. Remember that immobile ships are already prone to long-range blasting (heavy plasma loves them) or high-damage, short-range weapons that they can’t evade.
I think improving the AI will make this less of a concern. Make ships try to stay at range, or get in under the enemy’s minimum range, either of which could beat a slow ship. Give slower ships the disadvantage by making mobility an important part of the strategy, rather than just making a “beat all immobile ships” weapon.
Yup, getting ships to keep as close as possible to their assigned range while still moving around would help a lot. Missiles actually seem to work adequately well against immobile/super-slow fleets at this point, as long as you don’t use the Keep Moving order (and I guess assuming that the enemy isn’t also using missiles). Anything shorter-range than missiles will want to be moving while shooting, though, and right now that’s a pretty haphazard affair.
Weapons that are highly effective against totally stationary ships might actually be OK too, as long as they are balanced reasonably. In particular, they would probably need to be comparatively short-ranged, to allow for long-range ships that just happen to be stationary while shooting to start trying to back off when attacked. There’s still the question of ships which have had their engines destroyed, though - does it make sense to penalize disabled ships even further this way? I dunno.
Bottom line, if engineless designs are going to be permitted at all, I think it’s a bit of a complex issue that will require a multi-pronged solution.
I’ll echo a few of the other posters in saying that I don’t think there should be a superweapon that can automatically kill ships that stand still. I do think long ranged, low tracking speed, “siege gun” style weapons have a valuable place in the game, but they shouldn’t be dramatically more powerful than the ones already in the game. A bit more powerful, up to maybe double or triple, would be fine, since their low tracking speed will mean they miss a lot if their target is moving. If they were added, it would be important that to be sure the targeting AI was smart enough to fire on slow moving ships (either with an order, or by making target speed vs tracking speed part of the standard target selection algorithm).
In some ways the Heavy Plasma Launcher has some of the interesting characteristics of the weapons I’m talking about already, and I don’t think it would be a terrible idea to take it all the way by giving it a range of something like 1500-2000 and a tracking speed of 0.2-0.3 (subject to balancing). It could also be super heavy, making other Heavy Plasma ships it’s natural targets :-). Currently it feels to me (a player has not yet made any plasma spam builds that were any good) that Heavy and standard Cruiser Plasma Launchers are almost interchangeable, with identical DPS and very similar ranges and penetrations. More extreme differences in their stats would make them more interesting to play around with.
I think a long range stand off weapon is needed to counter the engineless ship. However I don’t think slow tracking speed is the answer. Instead I think Plasma should have its hit chance tied to the maximum movement speed of target ship and distance between the shooter and target. The idea being that ships can lob big chunks of slow moving plasma at each other, but the target ship usually dodges out of the way. Even if the target ship is not visably moving it can still dodge on the Z axis (unless it doesn’t have engines).
I’ve always thought that a ship’s max speed should account for some evadence
In which case the engineless ship will mount them.
Fixed casemates always beat mobile units (because the space/power/effort not used for engines can be re-used for armour or weapons) in straight combat. Unless
weapons and/or armour have arcs, so that slow/fixed units can be flanked
victory is strategic as well as a straight survival/kill counts/last-man-standing. e.g. if the mission is to get 25% of fleet from left to right-hand edge, an engineless ship is (almost - not quite if you’re really sneaky or lucky) useless.
Immobile units can only guarantee an advantage against mobile units if they’re engaging on a one-to-one basis. Mobile units, properly deployed and ordered can gain a significant advantage by gathering superior numbers and defeating the enemy in detail.
Simple suggestion… and please forgive me for also jumping in to beat this poor bloody equine corpse… but why not simply add an order that causes your ships to not engage (i.e. not move in on) immobile enemy targets… then make sure that in any battle where there is a stalemate because the ships don’t engage the team with more engines wins.