What some of you were thinking of, and what Gezza described, is called a Nexus. It is indeed found in Excelcia, as well as Freeworlds. The thing about it is its for total conversions. And ones that are very faction-aligned. Such as Freeworlds, and how you get Imperial or New Republic reps. If you pick Imperial, your red with New Republic. Its possible to get the NR neutral on an Imperial rep, but would take weeks.
But these are for mods where you start on one side or the other. Discovery keeps you in the 'freelancer' part of the game. Allowing you to start nearly neutral to many factions until you go out and sculpt your rep list.
Also, it takes the fun from gaining that rep. Sure a rep might be a pain to get in a few rare cases, but I could even get Xenos rep with 2 missions and about 5 kills outside of those missions.
The people who are determined not to RP and get everyone neutral could whether we had a Nexus or not. Because the reps can be changed easily, just by killing enemy ships. Also, Excelcia and Freeworlds don't have quite as many NPC factions as we do. Excelcia gives only a few bribes out, and Freeworlds only has 15-16 different NPCs. Discovery has dozens. Can fit that many NPCs in there and be able to use them all. Certain NPCs would block other ones.
I believe total neutrality shouldn't even exist in Discovery, but there are some that like to just trade. They don't do anything with their money, they just like trading and seeing/talking with other people online. Telling them to play SP if they want to play isn't a solution, nor polite. They like the interaction with other players, without dealing with every NPC and its mother.
Also, we cannot edit hardcoded parts of the game. We don't have the source codes to Freelancer, and I doubt it will ever be released.
And making massive addons and improvements FIXES most of those errors made by the game designers. While expanding a few. But making large illogical, and badly placed changes to the game will multiply those errors drastically.