I used them all for as long as I could and then I played the double agent.
After doing every BoS job I could without advancing the main-story far enough to severe ties with other factions, I started with the railroad. Doing all the butcher missions and even Tinker Tom's MILA jobs. Everything I could get my hands on. All the while still doing the minute men jobs as well.
Once the railroad began thinking about taking down other factions. I decided to work completely for the institute and minutemen.
Eventually "Father" asked me to wipe out the railroad. I went their and before doing it, I decided to do one more job for the railroad. Which was to take out the "Brotherhood of steel". So, I wiped out the Pryden, and then turned in the quest for the railroad, and then wiped all of them out for the institute. It was beautifully executed and I was able to do just about every single mission for all three factions.
The railroad are completely dead. I never see them anywhere now. I'm 150 hours into this play through.
Obsessionally. I'll run into a squad of BoS, but never any vertibirds or anything like that.
As for the institute, they have 4-5 characters that give out radiant never ending quests. Jobs that are either go fetch something, or someone, or go kill everything.
The really good thing about the institute, is their tech. If you scour through the facility and take all the items, you wouldn't believe how much rare quality junk items you can get. The loot in the institute blows away every other location, by miles. One example. Nuclear Material. A prety rare item with only one vendor ever selling it as shipment, and its super expensive and rare to even get. So player try to grab it one by one as they loot dozens of locations and vendors. If you're the leader of the institute, you can just walk around the facility and find loads of it everywhere, in all the pristine tools and devices that regularly respawn in various labs, and storage rooms. A bonus of being the leader, is that the entire facility is yours for the taking.