Oh, and I made the benefits GREEN now so it's easier to see which ones are best to go for first. 
I just wanted to point out, the rare goods benefits you are listing on the main post are not new to 1.2. In fact, Vega was the last stop on my rare route (if not already full) for a long time because it was close to Altair. Terra Mater I didn't stop at because of the black market requirement for those blood bores. So that's not what they added. My guess is that whatever was added isn't actually working at the moment, because nothing seems to have changed. Or, that what they added is so subtle, like a small repair or fuel discount, that we just aren't seeing it.
In most cases, he's pointing out what's available once you get the permit, not necessarily what showed up as of 1.2, so folks can decide if a given system is worth grinding the rep to gain the permit.
Alioth benefits:
Irkutsk station - ship discounts - Orca costs 38m, Asp costs 5.3m. Very beautiful and clean station, palms grow around docking bays, worth visiting.
All minor factions belong to Alliance, easy to build up your Alliance rep.
Phekda:
Nothing interesting. Shipyards empty (0 ships), outfitting has only 2 useless lowend items.
Gonsalez station has slaves, imperial slaves, narcotics, personal\battle weapons supply.
So, it seems no real benefits in Phekda. Maybe the system is just reserved for future storyline. Or maybe I missed something?
So if I understand this correctly, there is no reason to rank up in Empire, unless you want a Clipper. Yes?
edit* 14 Mar. Confirmed Summerland waste of time. No conflict/RES.
To be fair, conflict zones are a function of local politics and/or CG events, not something you'd gain from a permit to that system.
What about the Alpha Hydri Permit? Any infos on that?
Checked you list. Typos: Takura => Takurua. Cleos => Ceos.you can add Te Kaha, HIP 8396, Takura, Almagest, Robigo, Cleos and Sothis for sirus missions
these are the new colonies added to game and are all run by the sirus corp missions are available
Vega benefit:
Fort Dixon: beautiful palm tree station
you have to make rep with feds first, no matter if you have that merc edition.Maybe you guys can answer this one then ... I recently visited Sol so I could do the Earth/Mars/Pluto run and have a good look around the system but I never obtained a permit to do so! Now, I happen to have the Mercenary Edition of Elite: Dangerous - so would this account for my being there despite no permit? Never once while in Sol did anyone warn me off, or demand that I leave or try to blast my ship out from under me.