Ah! I see. I have a ton of them so i can't really sort through a bunch. But if i was to give the essentials i'd definitely say:
Legendary Modifications (Lets you put the legendary tags on weapons for a fair price)
Basically you still have to find other legendary mods, scrap them, and gain chips that you use to recreate the legendary mods on other weapons. It makes modding a bit more fun because you have to hunt down parts for legendary weeapons.
Vivid fallout:
Bethesda screwed up when it came to the textures... they put like 4k textures on everything, but stretched each texture out so far that it actually looks horridous. This mod lows it to 2k, and shrinks the stretching so it actually looks better + performs better. I run on a AMD 290x and gained like 15 solid FPS from it. from like 50~55 to 65~70. Its definitely worth having because of the fact that you get a better looking game + like 20% performance boost... i mean there is no downside.
Better Settlers:
Makes the random generated Settlers look better, come with random loot that is better. And look unique by opening up some of the random generation hair styles and gear color so they don't start looking like clones of each other after like 20+ people.
Homemaker
Makes ... making settlements more interesting, you get options that you didn't get before.
Robot Home defense:
You get to use assaultrons and other robots to protect your settlement instead of turrets. It's a good time.
Spring cleaning:
Warning: Using this mod might make placing things more difficult in the long run, so if you download it and activate it, use it and then disable it.
Basically this mod lets you get rid of all the random crap laying around the settlement that looks like it doesn't belong, but you couldn't get rid of before. Like the random toilets and trash, and piles of garbage in some spots.
However, a second warning... Bethesda really shows their master level level designing by ... having the level randomly break in some spots where the garbage was. So sometimes you'll clean a spot and it'll come out beautiful and you'll feel great. Sometimes you'll clean up a spot and it will be a clean hole through the level... It's a hit and miss. You'd have to save alot to avoid any real issues. but i've used it to clean my settlements to the point where besides the ground breaking areas, they look perfect. But to each's own if you don't want to tussle with the whole... breaking the floor bits.
Now some of these mods have requirements and etc etc. But I'm sure if you've modded before you can figure your way around. That and sometimes it will explicitly say, before you use this mod, make sure to do x, y and z. And they aer usually pretty simple instructions. Let me know if you run into trouble, have questions or have anything mod related you want to share.
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As far as the institute goes, so what you're tell me is that... i could've made them see Synths as more than pack mules?