I think your first playthrough should be mod free. I'm not saying mods are bad but you should experience the core game one time and perhaps enjoy the mods even more for what they are doing the second time around.
I, for one, have played the game thrice through without mods and been more than happy with it.
You don't have much experience to invest when you start a new game but it is a good time to get some basics down. I often start with one point in swimming, lockpicking and/or electronics. This is really all you need for these skills because one point in swimming is enogh to explore all the underwater passages and as for lockpicks and multitools, you will be carrying about 20 around most of the game.
I found I would get low on lockpicks and multitools if I didn't have at least two levels in each skill by the midgame.
I've never bothered with Swimming. I haven't challenged the conventional wisdom that Swimming is a crap skill in Deus Ex. Keeping one rebreather around and using it at the end, not beginning, of your lung capacity tends to be all you need. However, see my footnote!
Many people like hacking and will go for one point in computers and max out at two levels early in the game (the last level is wastefully expensive)
Seconded. I have sometimes maxed out hacking just because I wanted to, but no other reason to speak of.
The only skill well worth maxng out is Rifles because it gives great bonuses to the best weapons in the game (assault rifle, combat shotgun and sniper rifle).. Pistols are fine at one level, as is melee (stealth attacks from behind usually kill outright anyways).
This actually comes down to playstyle. I've played through with melee and relevant weapons and been very happy with my lethal options, but was only able to reliably deal nonlethal damage with pistols. In the late game, though, relying on pistols often requires some very fancy effort in order to avoid combat, or at least to avoid direct combat. More importantly re: melee, though, you'll eventually have a weapon which renders this the single most reliable damage-dealing skill of the lot, being far faster and cheaper than heavy weapons. It can even be used to open doors almost as effectively as explosives, and far more quietly and safely.
Okay, so it doesn't SOUND quiet subjectively, but I've found melee is usually a safe way to open things up.
Explosives play such a small role in the game you really should not need to invest in them.
Heavy weapons too play such a small role in the game but can be fun to dump points into, or at least upgrade once to increase walking speed if you want to actually use them for something other than "opening" doors.
I might recommend pistols and heavy weapons. The pistols should be useful through 2/3rds of the game, and the heavy weapons will become more plentiful and effective down the road. This is untested, though, and is simply the best I can come up with to render heavy weapons useful, 'cause dammit, rifles really do rock. Rifles and heavy weapons? Even if you invest in both, you'll rely on rifles too much to enjoy the flamethrower or Guided Explosive Projectile Gun you can't carry.
Lastly, there is medicine and environmental training. Both of these are quite redundant because there are so many other better options for healing, turning invisible and soaking up bullets. Then again, they are cheap so you can probably afford one level.
They are, however, functionally mutually exclusive with their respective cybernetic options, particularly environmental training, hazmat suits, and environmental protection cybernetics, or same training, ballistic armor, and the nano-augmentation of bulletproofing. They simply don't stack well.
Besides for making hacking and guns much better, skill points aren't very important in this game. It is with nano-augmentations that you REALLY build your character and define a playstyle.
Both true and untrue of the melee approach, since a strong melee build requires the cybernetics which are best-suited to dealing direct physical damage and also allow you to get close enough against tough, well-armed opponents.
Weapons to avoid? Don't go around bashing and slashing people in the face because almost everyone in the game will shoot back and kill you with a single headshot at that range.
That's where nano-augmented bulletproof skin comes in. Late game, I'd be more worried about enemies wielding explosives or poison, and there are nano-augmentations for those as well. See my footnote below.
Also, heavy weapons are quite pants for actual combat.
I'll take his word for it. I've yet to give them their proper try.
The sawn off shotgun is quite bad too because of the ridiculously short range (the return fire will be aimed at your face as with melee weapons).
See above re: melee and nano-augmentations. Myself, I found the shotgun was lethal to its user mainly because of noise and reload time. Damage output was okay, and range wasn't a problem for me. Nevertheless, best save the shotgun shells for the assault shotgun. Note these both use the Rifles skill.
If you want to shoot your way through the game, an assault rifle or combat shotgun is what you want. This game is not a shooter however, so you might want to consider playstyle options before deciding on weapons...
Au contraire, it can be quite the shooter if you want it to be. I felt awful for it, but my bodycount with an assault rifle was tremendous. See that mysterious footnote...
The game goes out of it's way in the first level to teach you that the non-lethal way is the most silent (which is completely illogical in a real world sense) but the game stops caring about enemy casualties after this level.
It notices from time to time, actually. Besides, the game's story and content actually push nonlethal takedowns for other and far more interesting reasons. You might find the game compels you... to feel.
The game does not award non-lethal takedowns in any way.
Nor does it reward lethal
takedowns in any way, because:
What it does however is award stealthy play. Avoid conflict altogether by finding hidden passages like air ducts and locked doors. This nets you some minor experience points
...which feel awesome to get, by the way...
but more importantly some encounters will impact how other characters react to you. It is not a bad idea to go play it as stealthy as you can and only using non-lethal takedowns because incidentally they are the most silent (even a baton to the back of the head is more quiet than a knife, somehow).
It's true, the game does reward stealth quite often, and some of the people you will meet will pressure you either to kill 'em all, or to use that lighter touch and do the least harm.
Among the rewards of stealthy gameplay, though, is getting to know your friends and foes better. They talk
to each other. They sometimes are very interesting and educational. Stop, listen. There's so much there. In a game so steeped in information technology, it's no coincidence how much you can intercept only by word of mouth.
The game is actually very easy on all difficulty settings if you go for all-out stealth. The difficulty settings only make combat more difficult by making enemies more accurate and damaging. Because of the wonky shooting mechanics in the game, it feels a lot better to play it as a stealth infiltration game where you only shoot at unsuspecting enemies or knock them out with a blow to the back with a melee weapon of choice.
Eh, headshots with an assault rifle or mini-crossbow are oddly satisfying as well, though there's nothing quite as disturbing as finding a good perch and taking down your opponents with a sniper rifle one after another like some kind of classified Charles Whitman.
Don't be afraid to try something! Stealthy gameplay doesn't necessarily require a nanoaugmentation for stealthy running. It may be just as useful and fun to take the nanoaugmentation which grants you the ability to jump high and land safely, since that can put you well above the fray. If you want to try melee only with found objects, such as metal boxes, try it! If you want to redirect enemy AIs by throwing darts at the wall or putting up walls of crates, try it!
Don't be afraid to try something, 'cause you never know! You can climb the walls by jumping atop explosives you've clipped to it. If it's not too high, you can even jump back down and collect them again.