I think a lot of us are feeling the lack of support for less-than-moral characters. Sure, karma is gone, but I don't really think that's the issue at the core: the game just doesn't support/promote a criminal life style at all. I'll have a few topics incoming, but I think this would be a great first step.

Allow raiders to take over settlements. It's a decently sized task, but one that I think is doable.

First, when Preston announces a new settlement, you can travel there and be approached by a raider when you near it. You can either side with the settlers or raiders at that point. However, this doesn't have to be a permanent choice. Anytime the settlement is flagged for a raider attack or quest, you can choose to side with the raiders if you want. Likewise, Preston can assign quests to you to take back the settlement, which you can side with either party.

Think of the quests! Instead of saving people or taking care of a raider problem, you could get quests to jailbreak someone or kidnap someone. Raider clans are often independent of one another so having non-hostile raiders in your settlement wouldn't necessarily make other raiders friendly (not that a raider is ever friendly). I would also suggest that 1) Raider settlement supply lines are separate from settler supply lines, and 2) Preston is completely oblivious to your actions unless he's an active companion. I can imagine quest turn in could be something like:

Preston: Hey, how did that new settlement come along?

Me: Unfortunately raiders have taken over the settlement and driven off the settlers.

Preston: Damn it! We're never going to get the Commonwealth on our side unless we can show we can protect people.

Wouldn't you siding with the Raiders likely get back to Preston (or any other "lawful" faction) and create some "issues"? While I'm not saying it wouldn't be an interesting situation, but it would be highly complex in terms of factions, companions and even resource sharing between settlements.

*wobbles hand

It essentially would operate much like how the game already operates - your companions are completely oblivious to your actions unless they're your active companion or if they're close by (think of giving Mama Murphy drugs). Your companions wouldn't have an issue of you being in a raider camp or building stuff there - just actions you take on their quests like kidnapping someone. Now that I'm thinking about it, since most of the companions want you to stick to the good path, you could make raider quests reward more caps and XP, to make the lone wanderer perk and play style more attractive (maybe it is already, I just don't take advantage of it). Outside of that, the main benefit of raider settlements would just be for RP purposes and access to different quests. Who knows, maybe they can add a raider companion (I'll stop there since I'm veering off track).

I addressed Preston's reaction at the end of my post as well as the sharing of supply lines - simply put, settler supply lines and raider supply lines cannot operate together, but can exist as two separate networks.

BoS hates ghouls, synths, and muties. I'm sure they could look the other way if the raiders were supporting them (especially since it's added firepower against the others). The railroad needs all the help they can get. They may not like it, but I'm sure they'll accept it. And...

At the end of the day, I think a few throw away lines could easily address how the big factions feel about your choice but ultimately accept it.

Well if the raiders/mutants/synths etc etc, were to take them by storm because you didn't adequately defend them, now that's something i could get behind. Having to take them back by force, that would have been cool. Not quite what the op was saying, but something I would have liked to have seen.

Actually, that's right in line with my original comment

I think it would be a mistake if implementing this forced a permanent decision. So I think if you let raiders take over a settlement, Preston will give you a quest to take it back which you can either take it back or betray the settlers. And hey, if no one's left alive, who's gonna tell Preston what really happened? }=>

Just let the Gunners replace the Minutemen as the 'take over the CW' faction

All Preston does is give you quests and fall in love with you. The Minutemen aren't a super detailed faction, they're just kinda... there.

You know, it's so funny you mention that because I was going to add a throw away line at the end of the OP, suggesting that the gunners could be an alternative to raiders or even a third option (the morally grey one). I decided against it just to keep the idea more simple, but I totally agree!

As Charlemagne19 suggested before me, they could have been the ones harassing Preston and the Minutemen, since the two factions are at extreme odds.

At that point, you'd be able to choose between helping the Gunners, or helping the Minutemen.

Exactly, and it's something I want to expand on in a different post. Saving it for later though.

I actually would like to see something like this where Raiders, Super Mutants, Gunners, and maybe even the Brotherhood of Steel can take over settlements (except for The Castle and Sanctuary due to their importance).

I hope OP can make mods because I would love to see this implemented. One of my favorite things about FNV was being able to choose sides. Doing quests for the NCR, while secretly working with Caesars Legion, assassinating NCR leaders all sneaky like. Walk into the Boomer camp earn their trust then murder their leader in her sleep. None of this is possible in F4. This isn't exactly what the OP is suggesting, but it would add that freedom to choose.

I meant if they are your enemy. I don't support the Brotherhood of Steel and never will.

Which will be very hard to do... Making a playable Raider route is not an easy thing to do.

Unfortunately, I agree in this case. This almost would have to be a change coming from BGS. Especially if you want the other factions to be at least as deep as the Minutemen are i.e. quests, player interactions, etc. I feel like voice recordings alone would have to warrant an official patch from BGS.

Im roleplaying that my character is forming a nation of his own in the northwest of the map, heavily allied with the BOS and loosely connected to The Minutemen. Having some sort of territorial control aspect to it would add a lot to it, having raiders enroach at the borders or taking down the trade routes instead of just singular attacks on the towns.

But then what im imagining in my head for my RP thing is closer to a strategy game than just building a home in the capital and connecting everything through Brahmin caravans. Something like this would add a lot to it, and I hope we get to see a expansion of the settlement stuff in a future DLC. I'd love to set up patrols from settlement to settlement or even find some way to define a border.

If raiders can't take over settlements, what happens if they attack a settlement and win?

I like it but I think after awhile it should be harder and harder to keep playing both sides against each other and the game would prompt you to choose between the Raiders or the Minutemen after awhile perhaps based on Charisma level. It has the whole A Fistful of Dollars feel which would go great with my Man with No Name character.

i kind of like what you're suggesting but in the event of it being to extreme a change, it would of least been nice for settlements to get overrun and instead of "settlement under attack" you could have to go there and retake a settlement from raiders and free the settlers, maybe if you ignore it for too long the settlers would all be executed and reclaiming it will mean you have to advertise for settlers all over again.