I wanted to give my thoughts so far in a summarised form in one place, instead of posting them everywhere. Makes things easier 
In general I like the expansion. I was expecting to be a bit beefier:
- More particle effects (e.g. more/different missile effects as research progresses. Could also have different effects depending on whether you chose cheaper lasers or longer ranging). I remember reading that this (unless I dreamed it?) would happen but I haven't noticed it at all.
- More diplomatic options/flavour text/ AI requests/colonisation options
- Perhaps a few more minor factions.
- A little bit more music for the main map gameplay?
It's little things, but they add immensely to polish.
I like the mercenaries. They add an extra twist and a few surprises. I particularly like that there are mercs that add influence, research, production and not only fight for you.
Issues so far (some of them may have been carried over from before expansion):
- Some missing artwork and buildings not behaving as expected (Mercenaries; reported)
- Faction influence/engine colour changing depending on game (e.g. Iridium sometimes have red (usually Drengin) colour instead of orange. (base game)
- Surrendered assets colours don't change to new faction colour (Mercenaries; reported)
- Music in diplomacy screen when talking to the Arceans has an introduction that takes too long. So you barely get to hear it. In fact most races diplomacy screen music takes too long to really hear. Most diplomacy actions take only a few seconds (at least for me?) so I don't get to enjoy the music's full impact.
I like the Torians, you might already know they are one of my favourites. They are well done in the game, the ships and the buildings are well designed. Perhaps there aren't as many unique buildings (for all races) as in GalCiv2 but even there it took until ToA for races to be completely unique.
Finally, even though I like the Arcean shipset and the colour looks nice on the ships, some of the small/tiny ships are not well visible in the background of the yellow/orange nebula (the galaxy background not the in-game nebulae). I especially don't like the colour on the UI and the influence borders/minimaps. It's not yellow enough!!
I will add any more in case I find anything later, but those are my initial thoughts.
EDIT:
One more thing that I forgot to add:
Upon attacking the Arcean starbases (I tried when I was playing with the Torians) all the Beam weapons concentrated on the centre of the starbase, which made it look a bit fake, both in terms of graphics layering on each other and also tactic! On other starbases the beams all go to different places. I will try attacking the Torians with the Arceans and report back.