NOTE: I don't expect any of these to be implemented, just putting them out for discussion purposes. Afterall, "Expectation is the root of all heart ache"
For weapon balancing, is there any way to apply an inverse cost to units? By this I mean, that a Thors Hammer Lynx would cost more to build than a Thors Hammer Tiger, and thus a player would be incentivized to stick to Thors Hammer Tigers instead of Lynxes. If this was possible then we could effectively make it so that players would only build specific weapons on specific platforms. Though, this may not be possible to hack in, so it may be a pipe dream.
A way to additionally balance Acid Cloud vs ESG is that one might be able to research a technology that applies a continuous damage debuff to enemy units after the initial attack that lasts for a period of time after the fact. So, as an example, a Lynx get hit by an acid cloud, and they get a debuff of 1 HP damage per second for 15 seconds. In the grand scheme of things it wouldn't be much damage, but it may be enough to cause movement speed degradation or finish off a heavily wounded unit after the initial effect. Again, may not be possible, so probably pipe dream.
A different way for Eden to be differentiated against Plymouth's early advantage is to reduce the cost of their guardposts and give their guardposts the ability to fire over walls. Thus any weapon put on an Eden Guardpost could fire over walls, such as Laser or Railgun. May not be possible though to implement.
Another way Eden could be differentiated is to reduce the cost of Panthers and Tigers, and thus are incentivized to utilize slower units over faster units. Plymouth's weapons are all built around speed and mobility, so it would make sense that Eden would counter Plymouth's mobility by building sturdy units instead. Perhaps if the Panther costed less to build than a Lynx for Eden, then Eden players would likely stick to Panthers more than Lynxes. I'm not sure this can be done without research, but I do believe that it can be done with research. Afterall, the research to improve cargo trucks changes the resources needed to build them, so could be feasible for Eden units.
Plymouth is honestly more of a faction for surviving New Terra over conquering it like Eden does. Most balance changes for it, likely wouldn't impact multiplayer much as Plymouth isn't really a warring faction; yes it has many units that work ideally for hit/run tactics, but its more about protecting its people and adapting to the world they live in. So it may be best, for multiplayers sake, to avoid making too many balance changes for Plymouth, and focus on Eden instead.
Here is a thought for Scorpions: What if we removed the beam weapon and instead replaced it with a short-range EMP weapon? This way, packs of Scorpions and Spiders could be a significant threat to players as they'd be immune to their own EMP and allow the spiders to steal your units. I'd definitely use Scorpions more if they had an EMP weapon over their current Beam weapon. And, if players researched Arachnid Factory first, then learned later to build Lynxes, this could be an interesting balancing decision.
I always thought of a more "tanky" Arachnid, the "Tick", that would have a close-range (1-2 square range) attack that applied a long-lasting EMP effect, allowing other Arachnids to close in and do their thing. Kind of like the "Tank-Hunter" in "Dark Reign 1".
The problem with balancing for multiplayer is that most players will purposely remove any advantages Plymouth has. Plymouth is better at morale, but players engage Stable Morale. Plymouth is better at surviving disasters, but players disable Disasters. Thus, players purposefully gimp Plymouth. So any balancing, needs to take into consideration that any changes made to Plymouth's civilian population will likely have no effect on multiplayer and thus it wouldn't be dangerous to say make their structures well designed to survive disasters or improving the effects of say positive morale for their birth/death rate.
Another way to balance Railgun vs RPG is to apply a very short duration EMP effect to a unit hit by a Railgun. This is to simulate the "physics" effect of being hit by an object travelling at extremely high speeds. The effect would only last for 15 frames (so if the game runs at 30 FPS, it lasts for 0.5 seconds), but it would be enough to effectively stop the enemy unit in place for a brief period of time to simulate the recoiling effect. I say EMP because I can't think of any other ingame effect that would prevent movement and attacking. And it would be really short so that it only stops the enemy for a very brief period of time, and thus giving the Railgun a bit of an interesting advantage. May not be possible to implement though.
Another way to balance Stickyfoam is to make it that Acid Cloud will eat away at the foam, freeing any units caught by the foam. Yes, your units would take damage from the Acid, but at least they'd be free to move again. May not be possible though to implement.
I'm actually curious about something: Is it actually possible to restrict a weapon to only one chassis? ie Restrict starflare to only Lynx? Or Restrict Thors Hammer to Panther / Tiger?