First off, there are a few things I want to go over before we begin . . .
The only weapons you may use are the combat knife, crowbar, baton, riot prod, sword, and the Dragon's Tooth Sword. Using guns, grenades and chucking crates of TNT at your enemies isn't allowed. However, smashing explosive containers is allowed, and is in fact the reason it's possible to scuttle the superfreighter with a baton!
I don't bother with the combat knife and crowbar personally, the baton does more damage and non-lethal takedowns are quieter, the only real use for the crowbar is taking down Anna Navarre. The baton is an excellent workhorse and can get you through the whole game, but I also rely heavily on the riot prod. Its stunning function is invaluable if you need to take down a group of people, though it doesn't work on heavily augmented characters. You'll want to get the sword as soon as you can, but you get the Dragon's Tooth Sword so soon afterwards that it isn't useful for very long.
Augmentations will have a huge influence on your gameplay style, but none are vital to your survival. The only augmentation I forbid is Spy Drone, I've never used it but it sounds like a ranged attack to me. Aggressive Defense System can be misused as well. It's one thing to defend yourself with it, that's fine by me, but when it's fully upgraded you can use it to kill enemies from a distance. Beyond that, anything you wish is fair game.
If you intend to destroy the weld points with the Dragon's Tooth Sword you'll want the Combat Strength augmentation maxed out when you reach the Wall Cloud. If you choose Microfibral Muscle or Combat Strength isn't maxed out in time you can still destroy the weld points, but you'll either need to use your arms to move the large explosive barrels into place or, if your environmental training skill is at advanced, or preferably master, you can place a crate of TNT in front of the weld point and smash it by hand.
One very important point that Nameless Voice alerted me to is the fact that you have three slots in which to install torso augmentations, two slots for subdural augmentations, and you may install any combination of them. This means that you can install both Cloak and Radar Transparency, but you'll have to sacrifice Ballistic Protection. As Nameless Voice put it, "How can they shoot you if they can't see you?"
Another very important point is that Ballistic Protection provides very little protection. At level 4 you're protected from 65% of damage, which isn't enough for you to destroy the weld points by hand. On the other hand, ballistic armour protects you from 50% of damage without any environmental training, and a master is protected from 87% of damage. You can only be protected from a maximum of 95% of incoming damage, so there's nothing to be gained by maxing out both of them.
As for the other augmentations, I highly recommend choosing Targeting over Vision Enhancement, it increases the amount of damage you do and knowing your enemy's health status is invaluable if they're going to blow up when they die. You'll also want to get Regeneration as you're going to take quite a beating.
There is quite a quandary when it comes to choosing Power Recirculator or Synthetic Heart. There appears to be only one augmentation canister for them in the whole game, in Versalife's UC Chamber, so we're truly forced to choose between them. (If anyone knows of a second canister please let me know.) If there were two canisters I'd highly recommend sacrificing Environmental Resistance or Aqualung in order to install both. As it stands, I recommend Power Recirculation only if you plan to upgrade it, otherwise, you should get Synthetic Heart, which boosts all of your augmentations by one level.
The most important thing to remember is that in order to destroy the weld points on the Wall Cloud you must either have microfibral muscle, or environmental training must be at advanced, preferably master, because the weld points cause explosive damage when destroyed. The Ballistic Protection augmentation is not enough to keep you alive, even at level 4. If you plan to use the Dragon's Tooth Sword advanced training will be sufficient, but I highly recommend upgrading to master level if you plan to use TNT, as the combined blast is almost always lethal at advanced.
There's no reason not to become a master in low tech weapons as soon as possible, but unless you intend to scuttle the superfreighter using the Dragon's Tooth Sword, it's not actually required. I suspect that a true masochist could complete the game melee weapon only with low tech weapons at untrained, but believe it or not, there are limits to my madness, and I'm not testing that theory.
Once you get past the Wall Cloud, feel free to spend your skill points as you wish.
As an example of how to invest your skill points, on my very thorough screenshot run I started the game by downgrading my pistol skills to untrained, then invested points in low tech weapons, electronics, lockpicking, and computers. I upgraded swimming to trained early in the game, but still had enough skill points to become a master in low tech weapons after Alex Jacobson asked me to kill Anna, and became a master in environmental training just before I tackled the weld points. After that I upgraded computer and electronics to advanced so I could hack turrets, and because I was going through a lot of multitools.
Marecki had some good strategies that I couldn't place anywhere else, and they're far too handy to throw away!
A general note on melee attacks against groups of two people neither of which cannot be approached without the other noticing:
While it doesn't take a genius to figure this out, let me say it anyway, just in case: as long as you're unable to eliminate your targets with one blow of whatever weapon you want to apply to them, use the prod! Jump out on one of the guys and zap him; with luck he will go down, but even if he doesn't you'll have few precious seconds in which to take out the other opponent. I don't recommend switching weapons to finish off stunned (gassed etc. too, but it's not relevant to us, ain't it) guys, most of the time this doesn't work - i.e. they remain standing and eager to hurt you.
Triggering turrets when you have no place to hide from them for a while:
After you've triggered the alarm, go back under the turret and make it face in the opposite direction of where you want to go, then run like hell. This will give you precious few extra seconds before the turret can start firing at you.
Another strategy for sneaking up on two guys close to one another:
Sometimes the only reason why they both cannot be taken out quietly and without wasting prod charges is that once one has fallen down, the other notices his body; another problematic situation is two guys watching over each other's shoulder, so to speak. The solution? Make the other turn away! There are two ways of doing that, one for friends and one from enemies. In the former case, simply stand in the right place (i.e. where you would like the AI to be looking) and talk to the fellow.
The latter is a bit more risky: standing as close to the desired direction as possible, become visible for your target so that he becomes alert, then QUICKLY hide again (having objects to hide behind is very useful here); if you want him to turn more, wait and repeat the process as many times as needed. In either case, in most situations your victim will remain facing in that direction, either becoming unaware of the other crumpling down to the floor or actually opening a formerly-watched path of approach. Then again, there are a few fellows who do return to their original position having returned to their idle state.
TNT -- one additional tip provided by Nameless Voice is the Soda Can Maneuver, which is essentially a safer version of the above tip. It works with any item; simply throw it in the direction you want your enemies to move, and when it lands, they'll run to investigate the noise. I found that they would run to the location of the noise, stop and look, then move to a new location a few seconds later, so you need to make your move as soon as they stop.
I played with an older version Shifter regularly, though I haven't tried version 1.9 yet. The most important thing you need to know is that it modifies the arms augmentations, combining combat strength and microfibral muscle under the microfibral muscle name, and introducing electrostatic discharge as the other arm augmentation. The change to microfibral muscle is a huge advantage for the melee only player, and changes something that never made sense to me. I'm so strong that my melee attacks can handle jobs meant for explosives but I can't pick up a box??
If you choose electrostatic discharge, on the other hand, you must heavily invest in environmental training, because the only way to blow the weld points will be to place crates of TNT in front of them and hit them. If you try that without any protection you'll leave one hell of a mess for the janitors. Even with environmental training maxed out I barely survived the destruction of a weld point. It is possible to survive at level three, but you must place the crate of TNT as far from the weld point as possible.
The Shifter mod also increases the damage done by the crowbar and sword, another happy, if perhaps a wee bit unfair, advantage to the melee only player! If you let Paul die, you'll also find a blackjack, an upgraded version of the baton, on his body during your escape.
HuRen creates a serious problem for the melee only player by drastically reducing the damage done by the Dragon's Tooth Sword, to the point that it cannot destroy the weld points. With non lethal maxed out it only does 72 damage, compared to the 150 damage it does in the base game and Shifter. To destroy the weld points you'll either have to use the aforementioned ballistic armour / TNT combo, or Nameless Voice's trick of scuttling the freighter with a baton, which only works if you installed the microfibral muscle augmentation.
Once environmental training is maxed out you'll probably want to think about investing heavily in lockpicking, you won't be able to power smash anywhere near as many locked doors after what was done to the Dragon's Tooth Sword, and you'll really start going through your lockpicks as the game progresses.