Everyone has pretty much got what I believe are the failings of the Settlement System covered, so I'll keep this short.
1) If I can transport junk and food between settlements with a Provisioner, why can't I do the same for weapons, ammo and armor? Surely this could be a Perk-thing?
2) Ability to create a 'refuge point' where Settlers will run for cover if you haven't given them equipment better than the basics they already possess.
3) Ability to create a 'equipment point' where Settlers will automatically head to and receive a 'Care Package', which is single-use item containing armor, weapons and ammo and maybe Stimpacks that you've made and put in the equipment point. One Care Package per Settler, they auto-equip all the items, you're not running around after every Tom, dike and Harry to manually gear them up so they don't get splattered across the floor by random Bloat Flies and the Settlers are actually somewhat capable of self-defence.
4) Snap-together function really needs some tweaking, it can be twitchy as hell. Creating walk-ways on the walls around your Settlements, rope-bridges between the structures, ladders leading to the roofs etc, this all needs to happen.
5) We need the ability to have a 'Clear All' and 'Remove Clutter' function. 'Clear All' wipes everything off the Settlement area, all trees, rocks, shrubs and existing buildings, and gives us the relevant salvage if you're sick and tired of forcing your Settlers to live in dodgy, run-down buildings with more holes than swiss cheese. 'Remove Clutter' removes all trees, rocks, grass and shrubs so things aren't clipping through your damn buildings all the time. I am tired of having to build everything on Cement Floors or Raised Floors just to have to avoid this because some dingleberry thought the Settlement needed a copse of unmovable dead bushes right where you need to build the bunk-house for your Settlers to spare as much farmable land as possible, or worse still, RIGHT ON TOP OF THE BIGGEST PATCH OF FARMABLE LAND.
6) Better Defences (1). Let's be honest, if you aren't blanketing your Settlement in Heavy Lasers, you're doing it wrong, but this has the side-effect of having most enemies turned into a pile of ash that lingers for far too long and is damn hard to find in the unrelenting muted greys, browns and ochres of the Wasteland. Either make Laser-Ash Piles glow like Plasma puddles, and I mean REALLY glow, or make it impossible for Laser Turrets to 'ash-ify' a target. I don't even want to go into how stupid the Rocket Launchers are with targeting and accidentally blowing up Caravan Guards, Brahmin and Traders because a Forged or Gunner ran too close to their camp ....
7) Better Defences (2). If I can command robots, and I have a sizeable amount of components to repair/upgrade/maintain them, then why can't I use my Hacking Abilities to send 'Wild' Robots to Settlements to serve as a mobile self-defence platform for that Settlement? If every resource counts and I'm fighting for the lives of these Settlers in a hostile, bleak hell-hole of a land, then why not supplement their defences with Protectrons, Mr Handy's, Assaultrons, Siege Bots and the rest?
8) NO MORE INVASIONS (1). If my Settlement(s) is built up to hell and has more guns that a Brotherhood of Steal (No that's not a typo) family reunion, then why in God's name are raggedy-ass Raiders going to risk going there to steal food, water and slaves? After the first few attempts and getting utterly butchered by the automated defences, let alone my legions of Settlers armed with flamers, heavy assault rifles and automatic laser pistols, even the most stubborn Raider is gonna go "Okay, too tough to crack, let's try elsewhere." and hopefully that'll be the end of Raider Invasions, which still leaves Super Mutants, Gunners and (depending upon where your allegiances go ...) possibly Synth and BoS Invasions to deal with.
9) NO MORE INVASIONS (2). The 'Settlement X is under Attack' message to not spawn when a random Synth infiltrator in the community starts attacking, and to stay up after they get insta-gibbed by my paranoid Settlers. Likewise, Ghoul Invasions to not spawn halfway out in the middle of no-where so the damn Feral Ghouls can get distracted by something shiny or get gibbed by a random wandering NPC, leaving you unable to complete the radiant quest. Have them spawn a short distance away, ideally just outside of the range of most turrets, and then they just start blitzing towards the Settlement with their horrific run animations that make it all but impossible to keep a bead on them outside of V.A.T.S..
10) Do you even english, bro? Clearer instructions for building and for Bethesda to actually tell us how 'population' works for a Settlement so we know if sending Provisioners 'to' a Settlement boosts that Settlement's population, or are the connected Settlements all part of one big pool, or is the Settlement population only considered between two linked Settlements, so Sanctuary and Red Rocket are one 'pool', and Sanctuary and Abernathy Farm are a separate 'pool'? There's no point in running your ass all over the Commonwealth hoping to get lucky and find that randomly-spawning Level 4 Trader who you met waaaaaay back at Level 5 if there's no way in hell any of your Settlements meet the requirements to attract them in the first place.