4e opened up its own can of worms for sure.
Off the top of my head, these are issues with 4e.
Matrix hacking is not character centered. Meaning anyone, no matter the build can hack with equal effect. (Its all equipment based). Which coupled with the changes, means people spend more time worrying about being hacked than actually hacking (see the pages on pages of forums about this very issue)
The rules do not support "long term" character growth.
By the way the mechanics work, characters come out of chargen pretty much "maxed out" in their primary roles and with little room to grow their core archtype, leading to "wide" characters instead of "tall" ones.
(Meaning, gunbunnies don't stay gunbunnies, because right out of the gate, the have maxex skills in guns, so they are forcrd to branch out to vehicle, social, or other aspects. After enough play, you end up with a group of hyper maxex Generalists, with the team all having the same skills, and ranks)
Modding of equipment has left pretty much left everything but 3 guns as pointless...
Since every weapon could be modded with just about every option, guns in 4e became just "full auto, battle hardened cyberlinked barrets" why? Because you could, and nothing beats a full auto burst for 30p -18ap....
(Other gun options are the full auto pistol, and the full auto shotgun.... for concealability, and murder-hobo room clearing).
5e fixed some if this stuff, but also broke other stuff...