Basically, don't bother with regular settlement quests if you have Conqueror installed.
Well, I don't know that it is that bad. I mean one core feature of Conqueror is being able to kill Preston and friends. From a strictly vanilla point of view this already kinda of game breaking and we are in uncharted territory, For all you white hats out there who aren't tired yet of running favors for the Minutemen, the other core feature is prebuilt settlements. Seems pretty exciting and worth the growing pains.
Just some random thoughts...
If you are playing Conqueror, especially as a good guy, seems like there are a few important things to do.
First off save often. Especially before entering a prebuilt settlement and/or before speaking to Preston. (If you are playing survival mode, take advantage of the free beds.) If you end up getting a quest that can't be completed or doesn't make sense, reload, rinse, repeat.
When you do enter a settlement try not to talk to any civilians until you can confirm for yourself that all the baddies have been completely eliminated. When I first visited the prebuilt Taffington, the civilians had seemed to take care of all the bloodbugs. But I ended up getting jumped by one they missed that I think was sleeping in the bloated brahmin carcass near the north building of the settlement. I suspect sleeping baddies are the worst offenders here. Think the two ghouls in the cabin at Sunshine: they don't actually go hostile until
you get near them.
If the civilians do ask for help, turn them down. Enjoy looking after yourself. You've earned it after all your past play throughs wiping butts and noses. Savor their disappointment. They will genuinely seemed surprise you aren't willing to help. Plus, they'll ask you again and again for help. Take some time to size up the settlement and situation.
If you get a kidnapping quest, don't be a cheapskate and just pay the ransom. Consider it an investment in your budding career as settlement tycoon. Alternatively, reload until you get a quest to go kill some ghouls or super mutants.
3) Preston asked me to "Clear" Warwick, but there are no hostiles there.
Important to have a save to roll back to if a quest doesn't make sense or seems like it will be impossible to complete.
But, really? You let Preston
live? Really? You are just waiting for him to give you artillery before you turn on him, right? You wolf in sheepskin! (I'm only half joking.) It's Conqueror! The Minutemen are under new management. Show the commonwealth you mean business. (I'm still only half joking.) After playing for more than two years, and always ultimately being disappointed with any outcome that requires me to rub out any faction, I find it difficult to express the surprisingly pure and unadulterated pleasure I experienced bumping off the Quincey Five in the museum. Just chasing down Mama Murphy is worth the price of admission. (I'm not joking.)
4) Finally, there is a quest to provide water to Nordhagen, but there is plenty of water - 999, to be exact (probably the highest value it can show). I stored the two water purifiers, and now there's a negative number on the quest for the current percentage instead of the 0% the quest started at.
Ugh. These are the absolute most annoying quests. Even without Conqueror, just playing SS only, they are a real pain in the ass. The power quests are the ones that get me. Costs a sensor to repair the plot, but the percentages go wonky. You have to build a bunch of generators you don't need. It takes a shit ton of tiny generators to make up for losing a nuclear power plant. Uugh! I always end up rolling back a save and then avoid that settlement for awhile. I imagine things are even worse if you get one these playing with city plans (with which I don't have much experience), but aren't those settlements powered by magic? How do you fix that when it breaks?