There will be a major crackdown on people who violate the Prime Directive. There’s been entirely too much of that crap. Complacency in covering up a Prime Directive violation will also be punished.
Um…you mean complicity, right?
Yet when the chips are down, the aliens are kicking away team/landing party butt, and it seems that All Is Lost, it’s time to beam down the Ripped Shirt Kirk.
^ :dubious: ^
Or, better still: What they did with the Doctor on Voyager proves it’s possible for holograms to leave the holodeck and even leave the ship. Therefore, every ship will have projective holotechnology. In a military situation, it will create and deploy holosoldiers – the programming carefully designed to keep them nonsentient and therefore ethically expendable.
Plus the agonizer! Don’t forget the agonizer! 
Nothing takes a long time to build if you have matter-replication technology. Heck, with a big enough replicator, you could turn out starships like a fish laying eggs.
It’s important for both morale and logistics to have an officer on the ground with the landing party / away team / sacrifical drones; there’s someone on the spot to make immediate decisions. That’s what lieutenants do for a living.
I’ll expand the restriction to include:
Senior medical personnel (particularly the CMO and counselor) will not go on “explore hostile territory” missions as long as trained combat medics are available. Those who repeatedly do so will be strongly encouraged to drop their commission and retrain as a combat medic.
Also, senior medical personnel are not bridge duty officers. They shall not stay on the bridge taking up space that can be used by someone who IS a bridge duty officer.
Taking that in another direction: The bridge (and any other major command & control facility) shall be designed for maximum efficiency and effectiveness, never mind what that does to camera angles and group shots.
No, they have to fire at Wesley, not Will.
Keep the kids off the ships. As has been said many times before, Starfleet is a military organization. You don’t put a kindergarten on a battleship, you don’t put a nursery in a tank and you sure as hell shouldn’t put children on a vessel that will go into combat situations. In the episode Rascals, the Ferengi threatened the children. Exploratory ships, colony ships, even cargo ships could carry kids but not Starfleet vessels.
If the inertial dampers are strong enough to keep people from slamming into walls during normal course adjustments, couldn’t we fix it so getting hit by an explosion wouldn’t knock us out of our chairs?
Get rid of synthehol! Ten Forward would be so much more entertaining with an occasional drunken brawl. Let the beings start fighting, then beam them to a Holodeck (already running with a simulation of Ten Forward so they combatants won’t notice the disruption) where they can continue to beat the crap out of each other. After one of them is unconscious, you beam them to the brig (or sick bay if they are in bad enough shape). Do not remove their hangovers!
I’m speaking more of the battles where the two ships are at rest (and conveniently oriented with the same “up”) or dogfighting.
So now we’re getting practical?
I’d be willing to make an exception for Data. An exploratory away team in unknown territory is best served by crew members trained for that purpose, not by expendable officers and medical personnel.
Who will be kept permanently in the pattern buffer and used in place of standard weaponry such as armed red shirts and photon torpedoes.
Uh, why? The first “volunteers” will be inanimate lumps of iron. Once you’ve got it down pat with those, you move on to inanimate lumps of other materials, then things like flatworms, fish, guinea pigs, and chimpanzees. Only when you’re absolutely certain that you’re not getting zero chimps, and that the chimps you get aren’t split up into their Freudian archetypes, only then do you start with the human volunteers.
Instead of a single “ship’s computer,” every ship will have different computers for different systems with firewalls between them, so that one computer malfunctioning will not cripple the ship. Since humanoid reaction-time is limited a single central computer to coordinate all the others may be necessary, but the humanoid crew will have the means to sever its communication with any of the other computers at any moment.
According to the tech manual, the E-D already has that: 3 different computer cores (2 in the saucer, one in the engineering hull) any 1 of which can independently run the ship.
Just rename it “The Prime Suggestion”
Engineering specs to have better ratings for components. How many times has a mission been jeapordized because the Lower Starbord Ion Relay has fused? Either protect the sensitive parts with fuses as mentioned above, or derate things a notch or two to better handle overloads.
Physical power disconnects.
Break up computing into multiple machines. We don’t run a company today on one big honking server, why do that with a starship? The computer that whips up snacks in Ten Forward should not also be calculating weapons trajectories in a tactical situation. Split 'em up before someone punches in commands to re-aim weapons when everyone thinks they’re just requesting a sandwich with no mayo. The critical stuff should be air-gapped from the non-critical stuff, and the whole works washed through a hypervisor.
Backups, backups, backups! Where are the backups?
Remove the rocks from the consoles on the bridge. All they do is fly out when the ship takes a torpedo hit.
Out-fracking-standing!
I know it’s been mentioned before, but marines. Not idiot, barely armed Starfleet security, but armed to the teeth, well trained, slightly psychotic, devil dogs.
Anytime an away team goes down. A squad of marines goes with them. If there are any crew off the ship (and thus likely to get kidnapped, taken hostage whatever) there is at least a squad ready to go.
Ghod help anyone who beams aboard without permission. No one or two guys with pistols to greet them, these guys would deploy in actual effective numbers, and use tactics designed to repel boarders, rather than allowing the ship to be taken over by anyone with a transporter and more than four people to beam over.
Enterprise (the series) at least had the MACOs, why did Starfleet decide to downgrade, other than the need to seem all fuzzy and explorer
like?
My personal fave:
In all starships constructed from this date forward, the bridge will be located in the center of the saucer section (i.e., equidistant from the upper and lower hull surfaces) for better protection. It makes no sense to cling to the tradition of having it at the top just because it made for a cool transparent-dome visual in the original pilot.
The only problem here is that the Enterprise is an exploratory ship. It has always been my impression that along with being the Starfleet equivalent of a battleship, the Enterprise’s primary mision was one of exploration. That’s not to say I agree with having kids on there in the first place, no matter what the primary mission is. And not just kids either, any sort of civilan, with maybe the exception of techinical experts, but we all know they just cause problems anyway.
As to the OP, my main change has been mentioned, don’t pussyfoot around with threats, letting yourself get blasted, so you wind up having to use some last ditch out-there plan. If it is agressive, blast the hell out of it with everything you’ve got. So yes you have a limited arsenal of Photon Torpedoes, so what if you run out, hot foot it back to a starbase for replenishment.
Okay, good point, though I’ll cheekily point out that they’re already partway up the scale, with something better than duplication - replicating an existing matter pattern without a physical example to ‘copy’.
ETA: Can you imagine drawing that assignment… being stuck on a science ship in orbit of a forbidding planet with a strange atmosphere to conduct extensive experiments in duplicating guinea pigs with a transporter beam? (I admit, it’s probably my imagination that the guinea pig stage could take 20 years or so, but that makes me chuckle
If I remember my Voyager correctly, that was done only through the use of a piece of 29th century technology that has resisted all attempts at reverse-engineering or similar duplication. 
(Except maybe for that Borg guy.)