^ Actually, I think it would be standard practice for some starfleets (not neccesarily the Federation) to intentionally decompress their ships on entering combat and have the crew perform the entire operation in space suits. It occurs to me that a ship full of atmosphere and combustible materials is probably an enormous fire hazard and it's just safer to avoid the whole "exploding consoles" thing if there's no air in there to begin with. Shutting down artificial gravity would seem to be a safe bet too; no more bridge officers getting crushed by falling pillars.
A bit of a tangent, but since we're on the subject of a distant-future trek reboot, I would probably take a cue from Mass Effect and simplify all technology so that it's in some way related to subspace field/mass reducing technology. IOW, phasers would really just be weaponized deflector beams: you have a setting that can repel the target (or a portion of the target) at a hundred gs, or a more gentle 10Gs if you just want to punch him out and not neccesarily kill him, or a "disruptor" setting that switches back and forth between repulsion and attraction a hundred times a second, literally rattling your target with intense hundred-g vibrations. Some more vicious versions of the phaser might cause the object to accelerate at high speed away or towards the center of the beam, alternately exploding or imploding your target. Photon torpedoes would be similar: effectively, disembodied warp nacelles with their own engines and fuel supply that chase down their targets and slam into them at high warp.
No shields, not really, but deflectors would actually be part of the warp drive and would involve using a repulsive warp field to propel incoming energy/objects away from the ship at high speed. The main deflector would have a much longer range, and a starship could actually defend itself by turning its bow towards an approaching torpedo or ship and turning on its deflector, forcing the aggressor to keep its distance.