What first person shooter mechanics do want? We've had some similar discussion, but it's been rather focused on specific things. What about general mechanics?
OffenseNot much to say here that hasn't been said elsewhere.
http://www.stexcalibur.com/forum/index.php/topic,4615.0.htmlhttp://www.stexcalibur.com/forum/index.php/topic,4613.0.htmlThe short version is, fewer weapons with more features, more alien weapons but with overlapping functions since they're meant for the same jobs.
One good hit, depending on the setting and where you hit the body should be able to kill most things. So, damage based on point of contact, or at least limb of contact. Arms and legs should count less than a torso hit, and the head should count for the most damage.
DefensesI'm leaning to no shields, and maybe a light armor, but more a Call of Duty 4 like system. In it, if you're hit and rest a couple of seconds behind cover, you recover and can move again. It's like you only thought you were hit because someone else's blood got in your eyes.

It keeps the pace faster and you can concentrate more on combat. The armor is to explain how you can take a bunch of phaser hits without dying from the first shot. Although, some sort of Trek twist where you take cover to use a hypospray pain killer might be good if you got hurt too many times for the armor to be realistic. So, you could die if you take too many hits in succession like CoD4, or if you take lots of hits over time. No life bar though, your general condition should get worse in order to indicate if you need pain killers, but needing them will be rare even with plenty of damage taken.
AmmoI would like the weapons to have thousands of shots. We almost never see anyone reload and the closest indications to shot capacity we have is where eight phasers in TOS were used to lift a shuttle nearly to orbit.
http://www.projectrho.com/rocket/rocket3l.html#lasermagazine (scroll down a little)
The author of the page concludes that each phaser would have 9.3e10 joules. In TNG: "The Mind's Eye" Geordi and Data test a phaser Type III at 1.05 megawatts.
http://www.phasers.net/2360/type3.htm9.3e10 joules/1.05 MW = slightly over 1 day of continuous fire. That's 88,571 seconds of fire. Better yet, that's a thousand times more powerful than a rifle round per second, you don't need that much energy to kill a person so normal kill shots mean the weapon can last even longer. So, unless the story has us fighting for days straight on the same weapon, or frequently using the higher settings, we shouldn't have to reload, recharge, nor switch weapons unless a different design is more ideal.
RechargingWe won't need it, except in extreme cases, and if our weapon is dead then we probably don't have time to figure out how to recharge it. Just go find an enemy weapon before that happens.
ObstructionsCertain objects should be completely resistant to certain phaser settings (but not all settings) and will make for cover. Other objects, like bushes should let phaser energy fly right through and be nothing more than concealment, obstructing enemy view only. Better phaser rifles should have optics that allow you to acquire targets behind concealment and cover, and just like with a gun, if your phaser is strong enough and the wall weak enough, you can fire through the wall. Enemy weapons might have scrambling devices or specially set tricorders to counter such weapon sensors, making it harder to hit targets behind concealment.
Our characters should be capable of pull ups, and thus capable of jumping up to a low ledge and pulling themselves up to the higher area. That should go for anything lower than the pull up height, too.
Jumping shouldn't be too high, but if we get a running start, it should be possible to leap decent distances in order to cross gaps.
LevelingEven if it's minimal, I would like some sort of leveling ability. Something subtle such as tighter aim, faster draw, faster run, higher jump, faster repair, and longer endurance, and perhaps weapon qualification. We should be able to go to the shooting gallery or gym to train up the various skills. No mini-games please, except for the target practice. This is in addition to non-combat stats such as scientific, engineering, historical, and diplomatic knowledge and ability. Just because the personality of the character is fixed doesn't mean the skill sets have to be. Then again maybe it does, so those intellectual skills may be general knowledge rather than professional knowledge, but they would help open conversation options with people who are skilled in those areas. Okay, that last bit is off topic.