Is that settlements have very little reason to actually exist.

For example- The Hub was settled around an oasis, hence the Water Merchants, Black Hills was settled by Marcus and Jacob for the uranium mines. Redding for gold, Klamath as a hunting town, et veteran. In the Mojave, Novac is both en route to Vegas and nearby the Repconn facility, which is a source of salvage; Nipton rose to regional prominence by Mayor Stein providing prostitutes to the NCR soldiers stationed nearby and later the Powder Gangers; Freeside is where the displaced of New Vegas were forced; Boulder City was a concrete mixing yard until the Deathclaws occupied the quarry. And in the Capitol Wasteland, most towns are chosen for strategic defensibility- Rivet City, Megaton, Arefu, et cetera.

The settlements in Fo4 are one- too numerous- and second- have no reason to really exist. No mention is made of resources to be had nearby and no effects are had either- they simply are. No trade routes really exist, and most require fortune's worth of investment to make them defensible or productive. In real life, most of those would have never been touched.

If the settlement system was simplified to say ten important, strategic locations- i.e., a quarry settlement to provide stone for MM defensive structures, or a settlement along the crossroads of trade routes, or a settlement along a floodplain that gets a bonus to food production, or a settlement along a waterway that can link other settlements by boat, then I think the system would be better. Whereas a lot of settlements exist in absolute danger zones, and are difficult to properly defend without the plot armor/superhuman salvage abilities of the SS. A lot of the pre-built settlements make sense- but others have comparatively nothing to offer, strategically or otherwise, and there's way to many of them that it just clogs the MM radiant quests in a shitter.