Fan patch is super solid, I just finished a play through, do recommend.
I am okay with changing the system in Fallout Fen. It is just doing this is super embelematic of how Bethesda approach the license. Oh here is a thing from Fallout, let's take it, completely change it to the point where it is no longer anything like the old thing (for good or bad!), but let's keep calling it the thing because the name is what makes it Fallout!
It treats branding like a label you just peal off and resticker on to something. SPECIAL without skills is just a stock standard stat system (instead of a GURPS rip off with the name changed). Super mutants on the opposite coast from where FEV was released in an isolated space are not really Supermutants as they stood in Fallout. The Brotherhood of Steel that are actually Wasteland Paladins instead of isolationist tech hoarders are not really the Brotherhood of Steel.
It makes for a functional game and can be fun and good, but it is super shitty at actually being Fallout.
And the thing is, NV clearly shows you can do it in that engine. Obsidian really brought Skills back to the forefront, but nah just raw stats will do the same job and we will get to/have to completely overhaul perks while we are at it.
Edit - oh yeah. Of course Fallout 4 has a Dog in it. Fallout 1 had Dogmeat. Fallout 2 had K-9 and Dogmeat in a secret area to reference how Fallout is an homage to Mad Max. So that means every Fallout game has to have Dogmeat because a dog called Dogmeat is Fallout tm.