The one thing about the old way of doing the reps.. was how a pirate could land on a police planet / base and vise versa.. this just does not make any RP sense at all, and since TR will be about playing a role, it made way more sense to remove the bribes and empathy side of it.
Also it was totally possible to pretty much get white with all the factions, and since we are adding the faction bases for players to build, tech companies and traders also, it makes sense for only your faction and their friends, along with tech factions and traders, to be allowed to dock at their respective bases, and especially since you will also build parts to the base to allow your clan / faction to have their own ships, weapons etc.
This can also be limited to a specific faction for RP purposes. Freelance is old, and it has to really change a bit for players to be a little bit more interested in playing it again. If you could get everything within a few days again, by just doing simple rep changes, you would be extemely bored and think to yourself.. now what do i do.. and then you have no reason to even play anymore.
TR is a whole different way to play the tekagi's mod, and with the changes that are being made, we believe you will have a fresh new game experience with it.
Hope this helps a little with your concerns on the factions.
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