First off not sure what you mean by make Fallout 4 better there has to be an end to how much a company is willing to put into a game!
Secondly Skyrim SE engine and Fallout 4 engine are not the same - not even close!
Lastly, one of the things that makes modern games great is a player who actually knows how to speak!
First: larger map, more things to do then just go clean up ghouls, mutants, or raiders. Some decent side quests (where there is an actual quest) would have been nice... less money and time spent on 2 voice actors for the character and more for npc's (in said actual quests).
Hell even the dlc's were lacking.... oh want to clean up and island (that just gives you what 2 more settlements to take care of and a couple more types of monsters), and become a bandit leader (yawn).
So yeah, make the game better with more non repeatable quests that go twards making the game world better or worse, tie in better with the older games.... yada yada yada (they could have done a lot in an extra year).
Second: Beth games have been based on the Gamebro Engine since what Morrowind.
Why do you think it is so easy to convert tools over between the games.
xEdit - made to read the esm/esp scripts and everything else... tools made from this are
tes4edit (oblivion), tes5edit (skyrim), f4edit (FO4), and SSEedit (Skyrim 64) just to name a few (cause I can't remember the name of the fo3, fnv, and other versions).
Nif Mesh format has just gone thru upgrades since way back when, things have been added and removed over time.... but at the core it is still the same nif file type.
Textures have changed over the years at to what version of the game engine was used....
Oh and yeah there are is still the spell tree in the esm/esp's of fallout 4... and enchantments (what do you thing the legendary items in fo4 are they are enchantments that are attached to a regular item)... but hay what ever floats you boat.... think of it as a completely different engine with a completely different toolset (but you would be wrong as they are based off of the same engine at there core).
Third: Actually falls back to the first.... make the game better. You don't need the Player character to talk to make a good game.
Fallout 3: so so side quests, you actually do build your character the way you want them... you don't speak and you don't have a pre-made backstory.
Fallout New Vegas: go side quests, interesting story, you actually have no clue who your character was so you can go about making that character into what ever you (as the player) want.... you don't talk.
Skyrim: shows up on a cart being hauled in with some people that you may or may not agree with... you get to choose what you want to do.... decent side quests (ass loads of side quests) very few are repetitive in the way FO4's are, the only thing that was missing was the ability to side with the dragons and destory tamriel.... again you don't speak (minus shouts).
On the other hand Fallout 4: premade backstory, stuck trying to find a kid, talk but the dialog is all...blah.... story is blah.... side quests are go help this group defend against (raider, mutant, ghoul), go save someone from (raider, mutant, or ghoul) location, or help build up settlement so they can stand a better chance again a raider, mutant, or ghoul assault.... If you don't mind the mindless and endless killing it's okay.... if you want a story well that is at most 10 to 20 hours of gameplay from start to finish..... character is preset with background and blah...
Oblivion: never played it so I don't know.