I finally got around to finishing this myself.
1) I thought the espionage feel (including the Bond-ian credit sequence) really differentiated it from the main game. The level of tech the setting has should make spoofing identities very easy, and no one should be sure who they're actually working with.
2) I disliked that most of the side gigs were coin flips as to if you picked the 'right' option - give me non-mandatory activities that reveal what's actually going on or skill checks I can pass to determine the truth of the scenario. Having 50% of your options being against your wishes is just nihilistic. So is having a number of the 'good' endings resolve with the people involved dead regardless (the SovOil related gal gets killed in an unmarked spot on the map, and the farmer bomber presumably gets captured and gives you up, as V will later get ambushed).
3) Speaking of nihilistic, the new ending. Yeah, I get it, Johnny's song he plays to Kerry to prove who he or she is is "Never Fade Away", and V ends up fading away. Hah hah, very punk. But Arasaka gets knocked off their throne even in the new ending, so for the world as a whole, the Devil ending is still worse, so why does everyone (other than Judy and Misty) end up getting shafted the most here?
4) Also a bummer that 2079 is just the epilogue. AIs are confirmed to be loose in meatworld (the blackwall tech crafting mission) at least, so hopefully that's still the main thread, whenever and wherever Orion is set.
5) I have mixed feelings on the combat, as it funnels you into a handful of playstyles to be effective (short range cool stealth, long distance alert everyone and hope you pick them off in time tech sniper, melee range body berzerk, etc.) given the increased difficulty. Some of them only really start working well at higher levels too - e.g. I'd love to see the shenanigans you have to pull off to have the Level 15 character you start with in Phantom Liberty survive on Very Hard as a netrunner when Sonic Shock doesn't pacify groups yet.
Edit: 6) The game is still buggy as hell, both new and pre-Phantom Liberty bugs that still exist. My Nomad still never had Beat on the Brat trigger even after completing PL, and my Street Kid still hard locks up at various spots on the map when the system tries loading something up (probably NPC model related) even after installing PL. (It's not computer related as I completely reinstalled the base game, ran a fresh Nomad up to 50 doing everything but the last Beat on the Brat fight, then installed PL, and I still hang in the same spots on the map.)