For me, the biggest disappointments:
When you make a planet viable.. there's no real change of scenery.. I was expecting to see seas/lakes on Voeld and Grass/Forest on Ela.. felt abit of a letdown to just change the sky and the ground very slightly. Over time I hoped the worlds would have become, eventually, greener.
And the fact that there's no interaction with your Squad. Outside of 3 skills. I absolutely detest Console Ports on Pc Platform and ME:A stinks of console port. That people even buy a Ps4 or Xbox One is beyond me, but that's their mistake, why force their mistake on me? I want proper gaming.. not 3 powers because thats the best a console can do without going belly up in confusion.
Consoles have utterly ruined gameplay on the pc platform.
Romance! Ugly Faces! No mciro-management (no armor for Squad and so on)
Outside of the characters being actual soggy toast, this is my biggest gripe. I was not amused when I found out that I couldn't tell my squadmates to stay in cover without them breaking out of it in less than 2 seconds or tell them what powers to use. This was especially infuriating when trying to take down the Architects. Don't even get me started on the lack of armor/weapon customization for them.
