On my third restart on Commander difficulty. Really enjoying the game minus a few things that bug me about the early game, so this time I've decided to just load up as many mods from the workshop as possible that seem to fit in with the game thematically and don't push the balance too much into the players favor. Here's what I've got so far.
Increased Cover Bonus - Adds +10 Cover Bonus to low cover and +5 to high, works for both sides. This is the same as in Long War.
Stun Lancer Rebalance - Turns Stun Lancers into a more fitting light attack unit and lowers their crit chance.
DMR - A Sniper Rifle Option - Sniper Rifle alternative, more mobile, less powerful.
Tweaks - Makes certain items a bit more useful in late game.
Classmod - Fill all attachment slots on weapons, and all classes can use rifles and shotguns. This one could be overpowered if you managed to assemble a weapon with all slots fitted. Especially when combined with WUE below.
Remove Aim Assists - Turns off the circumstantial hidden boosts/debuffs to your squad and the aliens.
Sword Rebalance - Adds +1 DMG to all swords and a little AP damage to make swords better in late game.
Weapon Upgrades Expanded - Adds better stats to weapon attachments. Makes them useful. Work in progress, might be OP, but vanilla attachments might as well be superficial.
True Concealment - Mission timers don't start until you are revealed. Actual timer values are lowered to account for this, 7 turns instead of 9 for some missions, 10 instead of 13 for others. BEST MOD. Makes sense and adds a new layer of strategy to the game since you have all the time in the world to position yourself, but once you attack, you have less time to escape. The initial planning stage is a lot more fun and your concealment is a LOT more valuable.
Katana Pack - Adds a Katana and Wakizashi to the game. Alternatives to the original sword with stats that are about what you'd hope. Haven't tried them in combat yet.
+ All the Long War Studios Mods
SMG Mod
Muton Centurion
Leader Class Mod
My aim with these was basically to extend the firefights and early game deployment options, and eliminate some of the things that I felt were out of place like suicide charging stun lancers. All of them run together with no problems so far.