The follow-ups to Metal Gear and Duke Nukem at least were made by the same people as the originals. Hideo Kojima and Todd Replogle/Allen Blum III respectively. Some copies of Metal Gear Solid even included the original game.
Wolfenstein 3D only used the name for publicity. And for cheap too. Pro tip: don't sell your IP, license it. Especially if someone comes knocking on your door. If someone else wants something you have that means there's more value in it than you can see.
It was a different time. And maybe the original two games would be even more obscure without 3D. I'd also say iD tech for a while was the driving thing, not the franchise branding, as seen with Quake and its sequel. So always a negotiation.
Wolfenstein 3D only used the name for publicity. And for cheap too. Pro tip: don't sell your IP, license it. Especially if someone comes knocking on your door. If someone else wants something you have that means there's more value in it than you can see.