As Marzhin said, the early books had a lot of problems, that have mostly been resolved now. My main issues with 5E basically all tie into the fact that opportunities for customization have been greatly reduced from 4th edition. As someone who greatly enjoys systems like Champions, M&M, BESM, and the like, being able to tweak things to fit my vision is key to my enjoyment of the game. The main issues I've got with the new system are:
Priority System - I've never liked the priority system, as it basically forces people into certain routes, rather than allowing them the flexibility to choose things how they like. 4th edition's Point Buy system was much more elegant, in my opinion.
Weapon Mods - We haven't had the rigger book yet, but weapon mods got kicked straight in the balls comparing this edition to the last. I liked being able to mod a weapon to my tastes. To borrow from the Marines, "This is my Predator IV. There are many like it, but this one is MINE."
Technomancers - TMs got thrown in a cell with Bubba the Love Troll and sandpaper instead of lube. They went from being the swiss army knives of the matrix, though less reliable in their abilities than regular matrix users to being shoehorned into only being hackers and being substantially both worse at their job than deckers and less versatile than deckers. And they kept all the drawbacks that balanced their utility with a hacker's reliability in the last edition, making them even worse. Hell, there was an entire technomancer Stream (like a mage's Tradition) focused on rigging and interacting with drones, and now TMs can't even jump into a drone without Submerging. Any TM Riggers out there (and yes, TMs made some damn fine riggers in 4th) got the shaft harder than the 'stars' of gangbang porn trids.
Redundancy - Part of the problem with the Priority system and the changes to Hacking/Rigging is that they absolutely murder party redundancy. In 4th, it was easy for each person in the group to have a primary role, and then a secondary or tertiary role that they could step into if need be. When speaking of a Face, for instance, they're always nice to have, but what if they catch a case of dead? What if you have things to do at two places at once? Having someone who can step up, even if they aren't in the same league, can make the difference between a milk run and all hell breaking loose. Most teams usually only have one Matrix specialist. In a standard group of 4-5, you have Magic, Muscle, Matrix, Face, and usually a second gunner, especially if the mage isn't combat-focused. In 4th edition, a Hacker could pull double duty, rigging a couple drones, or a Rigger could hack if need be. That redundancy was utterly wiped out, which means if the Hacker or Rigger takes a case of lead poisoning, the entire run is dead. Before, redundancy allowed you to at least try and finish the run.