This may be because I didn't research what I was buying (promotional materials and video walk-throughs spoil too much of the fun), but I expected more exploration. I expected dialogue decisions to have consequences. I expected to be able to approach goals in multiple ways. Once you're in a mission there's very little in the way of variety. Harebrained Studios promises the next official campaign will be more open-world, but it just seems unlikely unless the core engine is revamped. So expect puzzles to be more like an old school adventure game.
The save system... or lack thereof
I didn't think the checkpoint system was an issue until I got to the extremely difficult last stage of the game (two of my team were dead and the surviving member was a very bad choice from the get-go). Holy shit the game got frustrating quickly. I still think that, overall, the checkpoint system isn't as bad as some people are saying, but it could definitely use some tweaks. I don't mind restarting a chunk of combat, but whenever I have to go through the same dialogue tree multiple times I wonder why there wasn't a checkpoint after the conversation.
The matrix is pretty bland
When you jack into cyberspace your avatar's avatar is just a neon wireframe. Combat in the matrix is nearly identical to combat in meat space. Want to know how to hack a server? Drum-roll please: you click on it. That's it. How exciting, right? However, once the disappointment wears off it is fun to simultaneously fight in meat space and the matrix.
At the end of the day I've played plenty of AAA titles with a lot more bugs and a lot less sophistication. Aside from a little bit of stuttering and a frame-drop here and there, the game is super sleek and super cool. The more you like cyberpunk (or Shadowrun) the more you should like this. I'm eager to try user-generated content for the game out, but I doubt there will be much to choose from for a few weeks.