Some of the side quests are gated by the main story quests, which is fine, except the game doesn't tell you this, and actually misleads you. This side quest has a level 5 requirement, but you won't be able to do it until you've progressed to the level 12 main story quests, etc. Like, you can't drop off the chics bag to her in Dream World until after the main quests takes you there, and you can't enter Stimtown til it does either.
My main issues are traveling between levels (the fucking taxi can't even drop me off at the elevator, have to run 300 meters, what the fuck am I paying you for?) And I don't really care for the weapon upgrade system. Late game, here's an awesome weapon, try it out! Oh, you spent all your basics, sucks to be you!! HAHA. And they keep giving you upgrade mats in the last mission, like, what, am I going to port out to upgrade and start the level over??
Another thing, the burst rifles (ABR and EBR) seem a bit OP compared to the full auto ones. Like, the dps is on another level. And, it's just a personal preference, but I would rather fire in "short, controlled bursts" with the option to spray and pray, then have to clickclickclickclickclick all the time.