(I also posted this in the thread "Gameplay - depth vs complexity vs 'fun'", as both threads seem to be about this topic.)
To answer the initial question, I would love the basic gameplay to be a 3D shooter (with 3rd person view), but not a mere 3D shooter. (And no, I don't like turn-based combat systems much, and Shadowrun Returns already tried this out anyway.)
Actually, the system used in Mass Effect was not a bad one to start with IMHO, but you could go further.
First, I would love the level of zoom to be adjustable at any moment. This way, you could have either a far view of the action (which could be very helpful for scheduling your actions during a covert op, for instance) or a view very close to the character (which could be very helpful during gunfights, or to dodge things).
Then, I would love the combat system to take into account RPG's elements, and not only being about shooting faster than the mobs. You could imagine, for instance, a semi-automatic lock (which locks enemies faster if you point your gun in the right direction, or if you have a lot of points in your gun skill). You could also imagine that the effect of cyber-implants improving the reactivity of our character would be to allow the player to enter a slow motion mode during a few seconds (useful for planning your next actions in combat) -but not pausing the game-.
Finally, since teamplay is important in Cyberpunk (as in most pen-and-paper RPGs), I would love to be able to hire teammates, that I could give detailed orders to in combat (a system similar to the one of Mass Effect).
(By the way, please forgive my English, I am French.)