I have no problem with new game mechanics, if they contribute alot to the game. And i dont see research or crafting adding much to that - at least not when compared to fleshing out the already existing game play elements first (trading, combat, production/building).I'm sorry but why is the "research thing" silly? That seems to be a personal opinion that for some reason you dislike the thought of Egosoft adding any new game mechanics to the franchise.
Why? Because the gameplay (the action) of conducting research is - quite frankly - in most games very very boring. You click on the thing you have and *pop* you got the thing you wanted (or more commonly: wait until arbitrary bar is full before, to "build excitement", before it goes *pop*). In mission-driven research it's not much more exiting. As there are a lot of technologies, you can't make a custom mission tree for every technology/product/whatever you "research", so they would be extremely generic and repetitive - Typical fetch quest, typical "collect 10 bear arses" mission, etc. Mini game driven research is the worst, if not considerable time is spent on the minigame - which ES clearly could not deliver because of how small they are. I'm even very sceptical, that SC can deliver people the "research" fantasy they promised them.
Research and crafting can't make a game interesting by themself either. They are like exotic spices... you wouldnt eat just some exotic spice. And you can cook most meals perfectly fine without relying on that exotic spice. If they spent a lot of time making research and crafting great , other parts of the game will receive less time. If they spent only little time on those features, they will feel slapped on and half arsed.
The core of the game (station building/production, trading, combat) is very expansive, that even in X3 and XR it was not where it could be, and in some areas it was simply flawed and unpolished. Now in X4 there is the addition of a proper map and RTS controlls...
Research and crafting are content gating. Content gating / unlocking can be achieved in other ways as well (buying or getting gifted licenses or blueprints for example). The wish that you don't need to fly all across the galaxy to equip all the software for one ship can be realised without needing any "research" feature at all.
Edit: Actually reading your initial post, you suggest getting rid of all softwares all together and having all ships have the same software automatically. Which i totally disagree with. It is a decision i have to make, if i spend the ressources to equip a ship with everything, or just with what it needs. In X3 this wasnt particularly meaningfull as ship upgrades where dirt cheap in most cases - this could be changed. Just giving every ship the same software removes this completely and makes the choice of getting a software a complete nobrainer. Also, what is with people that choose another playstyle than you? What if they build no HQ? Should those players be locked out of having access to good software?