1. My first concern is the Mirkwood Outpost. I believe it could be made more into a castle, like Lothlorien. You pay a bit more, say 1500-2000, and then it becomes like a Fortress in itself, instantly garrisoned by Mirkwood Archers and also able to build your default troops. Then, like the Lothlorien Castle/Fortress, it becomes a unique 2nd castle, instead of a second outpost like the Lothlorien Outpost. Similar to Dol Guldur or Minas Morgul, but cheaper and with build plots. This way, you would choose for a cheaper extension via the Lothlorien outpost, or go for a heavier playstyle with the Mirkwood Fortress. I will also propose a few changes to the buildings that are currently implemented, which would then be needed to accompany my proposals if we wish to create more uniqueness between the two, but more will follow down here.
2. Secondly, I believe that all leadership abilities should not overlap and be respective to their own realms only. For instance, Thranduil's first ability, King of Mirkwood, should only affect Mirkwood units. Similarly, Haldir's armour buff should only apply to the Galadhrim around him, or Lothlorien's basic units (that is debatable). This way, blobbing your troops together is less effective, and there is more authenticity and accuracy. What I see often is Mirkwood and Lothlorien's units being massed together, which would still be possible according to my suggested revisions, but it would be much less cost-effective. It would be thus more cost-effective to have both armies only join the battle together if you need more ''Firepower'', but otherwise, it would be more cost effective if both armies fought seperately during an actual game, on multiple fronts.
3. Thirdly, I am concerned about Palace Guards. Lore-wise and gameplay-wise, I do not think they are in a good spot right now. They feel and function too much like Tower Guards but without the Shield Wall Formation. As we all know, Tower Guards are a unique Gondorian unit and they should remain exclusive that way. I propose to replace them, with a cheaper alternative.
This: http://www.moddb.com/mods/rc-mod/images/heavy-mirkwood-spearman
Since you already have Valaquenta's/NewErr's Mirkwood Swordsmen and Archers models, I believe it would be logical to include this one too. At the cost of 300, they shun heavy armour, and are more affordable on the field. That is Mirkwood's job after all, to have a sustainable army on the field that can transition into late-game, akin to some kind of Elven Gondor. Mirkwood's units do less damage in general compared to Lothlorien and that is good, since they are more defensive and do much better in slugfests with their unique formations.
However, Mirkwood's glaring weakness is of course cavalry, and I think Palace Guards are too slow to protect your archers effectively. With the Mirkwood Spearmen, that comes with a unique formation, like the other Mirkwood units, you can get two of them out at the price of 1 single Palace Guard squad and they can form a line.
Furthermore, unlike the White Company and the Regiments of Tower Guards that would accompany royal members of Numenorean descent into the field, Palace Guards did no such thing. I believe Thranduil would have them protect the hall from the evils of the forest at all costs, unless given an explicit order to do otherwise. As such, Palace Guards would not be removed, but re-allocated to a Fortress ability in the upgrades.
This formation I would like to call the Deflector Formation, where you can block incoming arrows and cavalry in a narrow/small path, and protect units if you place them behind the Spearmen that are in formation while the Spearmen take 25-30% less ranged and trample damage. This is obviously reminiscent of the BOTFA movie, and it should make it easier for Mirkwood archers to be protected, if they stand behind them. Anything simpler is also welcome.
4. Elk Archers. While I am aware that they are non-cannon, I think that the idea is genuinely interesting, however it would be interesting to expand on them a bit. They become the Elite unit of Mirkwood, tied to a new structure, since Mirkwood loses it Palace Guards as purchasable troops. It also emphasises the archery nature of the Silvan Elves.
5. The changes to the buildings I mentioned, I would do as follows:
a. The Vault of the King is replaced by Elk Stables. Elk Archers become the Elite unit of Mirkwood instead. Instead of Elks coming out of the castle, it would be interesting if the Mirkwood castle thus had some kind of Elk pasture to hold them. It is not unheard of, having elk domesticised. They are ideal forest grazers. They also appear in the halls of Mirkwood of The Lego Game version of The Hobbit and Thranduil's throne seems to be made out of the horns of the extinct ''Irish Elk'' (Which is what his mount is based on). Surely, an Elk Stable does not sound so strange. Their cost could be increased if needed, to 700 or so, and they can stealth in trees to make them stand out a bit more compared to the Rohan Horse Archers. Each additional Elk Stable on a Mirkwood Fortress build plot, reduces the cost of them by 20%.
b. The Troop Chamber is replaced by the Mirkwood Forge/Armoury. Since the default troops have been moved to the default Fortress, reducing their costs would be unneeded, I think. Instead, the forges of Mirkwood now reduce the upgrade costs of Mirkwood's Silverthorns and Master Blades, since I doubt Lothlorien's forges would provide for Mirkwood. So, in that sense, Lothlorien's forges and camps reduce
c. The Wine Cellar remains the same.
d. The Upgrades that were in the Vault of the King, should be moved to the Mirkwood Fortress by default.
The Quick Recruitment ability remains the same.
I believe the Mirkwood Fortress should also get Silverthorn arrows as an upgrade, just like the Lorthlorien Fortress, if the cost increase is incorporated.
Now, The Palace Guard ability could be made into an active ability, where you research it, and then, like the Recruitment ability, you can temporarily summon several Palace Guard creeps around every building connected to the Mirkwood Fortress that will repel enemies. Some decent cooldown afterwards, of course.
Wine from Dorwinion (1000CP) upgrade should also increase CPs by 200-300, apart from the resource increase, just like the Outpost of Lothlorien.
6. The only leadership in the entire two realms that can affect each other, is the one from Lady Galadriel as a Ring Hero. Both Good and Evil. She is the most splendid Elf in Middle-Earth after all. She brings the two factions ''together'' so to speak, even though Celeborn and Thranduil negotiated after the conflict.
A final note: I am sure I missed a couple of things, but these are some of my thoughts on how to tackle the issue of Mirkwood being ''subjected'' to Lothlorien. The factions share similar mechanics, but with some key differences, the most notable one being the exclusiveness from each other's Realms, with the leaderships and the cost reductions. Also, all their ''Outpost'' can be turned into Elven Fortresses, which seems quite a logical way for the Elves to expand, if they would. Don't take these suggestions too seriously though, I enjoy Lothlorien and Mirkwood's current dynamic quite a bit as well and I type this simply for discussion material. Still, any thoughts or remarks are more than welcome.