I beat it the day before yesterday and I must say that I think the story was a bit lacking - the gameplay was extremely fun, however. Honestly I predicted pretty much everything that happened with major characters during the story though.
I wish they had included
-more ways to use hacking,
-less shooting,
-regular jumping rather then simply the climbing over things, more with dedsec,
-more with the serial killer side missions (The end of those side missions was complete ****)
-a more optimized PC version (Although I was able to play with relatively no problems. It's just a shame that the game couldn't be ran at 60FPS even with a GTX 780.)
-a less predictable storyline
-MORE WITH DEDSEC, FFS?
-less 'escape from the police' missions - they're pretty boring and on occasion rather annoying (expecially without Jam Coms)
-Better clothing options (Pretty much none of the clothing I bought looked better than the original - all of them pretty much had something that ruined them)
-I wish a particular event in the storyline didn't happen - those who played may know what I mean. Don't want to spoil it though.
-I wish they would stop pushing your character as a vigilante considering all the story line made you do is kill people, generally for selfish reasons.

LAST BUT NOT LEAST EVEN REMOTELY:
Why the hell did they make a DLC already with game-breaking glitches on the loose, a terrible PC port, and simply so close after being released:
http://store.steampowered.com/app/293057/