So, first some clarification for the current implementation:
Major and minor faction slowly decays over time to just inside friendly/unfriendly boundaries if above/below them.
This decay takes at most (if you're right at the extremes of reputation) around 20 days.
This decay only occurs when you are offline.
It helps Commanders to escape a potentially permanent hostility trap with minor and major factions.
It makes it slightly harder for Commanders to be allied with multiple major factions at the same time.
We've been looking at the various feedback and the system to see if there were any finesses we could apply, and it turns out that *maybe* there are.
What we're going to try out is the following change, which we think is an improvement:
Both minor and major factions will still slowly forgive Commanders who they are currently hostile with.
Only major factions will slowly lower reputation over time with Commanders that they are allied with.
Your reputation with a minor faction is a combination of minor and major reputation.
This system allows Commanders to become "heroes" with minor factions they put effort into supporting, helps Commanders slowly creep back from hostile status (just) and still allows the major factions to influence to drain slowly if you're not actively supporting them.
Obviously, we'll continue to look at how this plays out, including speed of decay, maximum decay levels and so on - the background simulation is still important to us, even with the launch of Powerplay.
If a minor faction is independent then once you become allied you will remain allied until you start annoying them. However, should you become hostile over time they will slowly forgive you and become merely unfriendly (assuming you don't keep annoying them).