You realize what you just wrote? I bolded the important part for you, so you can reconsider what you just said.
No, it actually makes no sense. The Section 31 lockbox is a very bad idea as it is, but a reputation, and I'm not being nasty on purpose here, really makes no sense whatsoever.
Diverting fleet resources to a shadowy organization? Is that what has become of the Federation? We're going to finance Section 31 so we can haz more ships??
Sorry, really makes no sense for me, every Star Trek Captain and Star Trek hero character I have ever seen worked to uncover Section 31, their plots and stop their agenda, all of them very pretty much disgusted with how Section 31 goes about it's work.
And I'm sure that's what the reputation would be, particularly associated missions. But you help them to gain their trust. Then at Tier 5, you betray them and take a noble stand. Of course then it turns out that they wanted you to betray them and that doing so helped them out.
Now... The rewards are a different story. You have evil rewards (just like how you have lockbox ships) to enable people to roleplay being something other than the typical hero in Star Trek.
The attraction from Section 31 is that they can do bad things. Say goodbye to the clean image of the Federation.
So far we have seen a reputation against the borg (omega), siege based (romulan) and science based (Tholian). An intelligence based reputation could be mighty interesting.
Reputation powers ala viral matrix and mask energy signature etc.
But it has been beaten to death already. Since DS9 Star Trek got "dark" and in the end everyone is evil (except the Bajorans) and STO got the cake with their warmongering, genocidal terran empire-esque federation. Basically every second mission is Section 31-influenced already and if it's not them it's some other secret-infiltrator-CIA-spy nonsense. I wish I could play a TNG federation or the real fed-klingon war...
much better if tovan =khev and drake fought to the death in space suits and BOTH died horribly
Not as over-used as the Borg.
There is NOTHING I find more boring in this game - they're everywhere, they are a GROSSLY overused cliche and they don't do anything other than spam Plasma and drain shields. They are a catastrophic bore!
The sad thing is that there are so many better options (STF wise) - use the Elachi or sometihng, but PLEASE, no more Borg rubbish!!
As for having Borg playable starships - I really don't get the motivation behind this. Playing as the collective as such is just not feasable, which means that the ship would have to be 'liberated' (a'la Seven of nine or Hugh's Borg individual group). But even then I don't see the point - 'flying' the very epitome of a space-brick would be about as entertaining as acute haemarroids!