I think I'm into a pretty different experience than most, so I'm not sure how helpful this will be, but here's my rebalance stuff;
Fallout 4 Loot Overhaul; don't like all the worldspace edits, but it's far and away (even though it doesn't cover DLC, which is an issue) the most comprehensive loot mod. And the worldspace stuff really is necessary to achieve its goal, unless that could be done by a script maybe like Project Nevada in New Vegas? Way over my head there though. Looking at maybe incorporating Loot Logic and Reduction to at least get a couple DLC lvl lists but there's no way it can replace Loot Overhaul.
Some Assembly Required; combined with Loot Overhaul, its something like Morrowloot+Scarcity for Skyrim, which are two of my favourite mods.
I'm sure you're aware of these two (they were both in the Realism section IIRC) but they're really the core of what I'm after.
Damage Threshold + Patcher
Fat Man Radiation Hazard
Impervious Power Armor
Ironman Survival Tweaks (I only use Adamantium Skeleton, Awareness Expanded, Robotics Expert and Shotgun Surgeon)
Level-Up Healing Removal
Moons Legendary Overhaul; I'm testing/looking at this right now, not sure if I'll keep. I hate the Legendary system in Fallout 4, and I'm not excited by most of the 'solutions' I've seen offered thus far... though admittedly I haven't actually tested any, just put off conceptually.
More Weaves - No Railroad
No Legendary Items from Creatures
No Limb Regen + Companion Fix
Rechambering Plus; Also testing/looking at this. I don't use Weaponsmith/Loads, etc. but like the added functionality here, and I like that it makes pipe weapons more useful. My ideal situation is one in which advanced weaponry is much more difficult to come by, and places a lot of emphasis on crafting. Y'know, destroyed world and all.
Weapons of Fate
Legendary Enemy Spawning; I use All Difficulties .25x and Legendary Rarity 5... haven't honestly tested this thoroughly to see how it actually works out though. Decreasing the overall amount of Legendary spawns while increasing the # of NPC's that can potentially be legendary...
Longer Area Respawn
No VATS Damage Reduction; 25%
XP Levelling Linearised-ish
And a couple for getting around in Survival;
Institute Teleportation for Survival
Lone Wanderer; used to use this, but cut it because of all the worldspace edits. I don't know how to patch that stuff so my current build has cut out as many mods that do as possible.