How would you solve the problem, without changing the game to isometric turn based or something.
Consistency and proper worldbuilding.
Nobody expects gangbangers to put up much of a fight, nor to be equipped well enough to challenge the player outside of the early levels of the game.
Police would naturally be more of a challenge. SWAT, Trauma Teams, corporate security and other such more professional outfits would have access to much better weapons, better armor, better cyberware and make use of more "advanced" tactics (amp up their aggression and have them throw grenades more often).
If you dump the retarded Diablo-esque weapon itemization and have weapons do consistent damage, it's easy to scale the threat enemies pose without turning them into bullet sponges. Street level thugs with the futuristic equivalent of MAC-10s aren't going to put up much of a fight, but corpo security equipped with smart weapons and big sniper rifles?
On top of that then simply add more unique types of enemies - ones that can cloak themselves, ones that rush you in melee, tanks, quick-firing enemies, snipers etc. and distribute them according to the overall competence and access to equipment according to lore. Introduce non-human enemies too, like androids, drones and animals to diversity the enemy roster.
