I'd say for 90 percent of riders out there a factory-built set of wheels is exactly what they need. Wheels from ENVE, HED, Industry 9, Hunt, Neugent, Rolf, Fulcrum/Campagnolo, Roval, Shimano, Mavic, and others still work well for a lot of riders, and for good reason: the bang-for-the-buck is good. On some lower-end sets the compromises will be in bearing durability and/or quality (e.g. steel vs. ceramic), hub weight, freehub actuation, spoke count, spoke type, etc. And the tradeoff of wheel weight vs. weigh capacity is still there: the superlight factory-built wheels mostly aren't rated for a total ride+bike weight over 220 pounds/100 kilograms.
For the other 10 percent custom is probably best. Think of bikepackers, folks on the higher end of the body mass spectrum, retro setups, and the like: there aren't a lot of factory setups that fit the bill. To wit: I know of many custom builders who get carbon rims and pair them with ultralight spokes and higher-end hubs to build to a rider's exact needs.
The wheels on my older road bike are custom-built on Campagnolo Chorus hubs (super easy to maintain, still using cup-and-cone ball bearings) with Sapim X-Ray spokes and Velocity A23 rims. They're not the lightest but they're on a par with Mavic Ksyrium Elites, differing only by 20 grams, but are much more comfortable as they have 32 spokes at a lighter tension than the 20 spoke Mavics. If a spoke snaps they're not likely to go super out-of-true. They handle washboard gravel without transmitting all the roughness to my body (note that tire choice and pressure play into this as well).
My backup wheels for this bike: Mavic Aksiums. They're heavier but they do just fine with proper care (the older Mavic freehubs develop play all too easily due to planned wear).
But the wheels on my Moots are a factory built wheelset from QBP: Shimano 105 R7000 hubs, DT Swiss spokes and DT Swiss R500db rims. They're not the lightest but given I take the Moots on almost any kind of surface they're built for the long haul. I'm thinking of getting a second set of wheels for this bike, and they'll likely be custom built with a mix of Industry 9 hubs and either HED, H+SON, or Astral rims, spokes TBD but likely butted and probably 24 front, 28 rear. Sure, I could get something factory-built but the cost will likely be the same and the weight similar.