I usually choose either Navy or Marines, depending on difficulty level. They're both pretty much the same, the only thing that's really different is the starting stats you get. So your choice of Navy or Marines is pretty irrelevant after an hour or two.
In the early game I usually focus Cybernetic Modules on Hacking (putting points into Cyber-Affinity whenever it feels like high level hacks are still too difficult), Research, Standard Weapons, and Strength.
As for the skills, in my opinion of them...
Tech
1. Hack: Not really mandatory, but it makes the game a lot more forgiving in the long run. Most notable bonus is access to supply caches that would otherwise be inaccessible to you. I typically max this by the end of the game.
2. Maintain: Fairly useless if you play pure melee, mandatory if you intend on using firearms. Firearms degrade so quickly that it's always worth putting spare Cybernetic Modules into this skill. That said, don't go crazy with it. Each time you upgrade it it'll increase the amount of damage on your weapons that can be fixed per consumable item as well as increase the amount of charge on powered items. I don't usually go higher than three or so points into this.
3. Modify: Completely and utterly worthless. Most of the weapon modifications in this game are garbage, if not inherently detrimental to you (example: Fully-Automatic upgrade for the assault rifle, resulting in it chewing through even more of your already fairly limited ammunition and degrading at an even faster rate). Upgrades do give small bonuses to the weapon's performance outside of the new fire modes, but it's still not worth putting the points into this skill since you can find consumable items called French-Epstein Devices that imbue one upgrade to one weapon (each weapon has two upgrade levels). I usually upgrade the Assault Rifle with my first two French-Epstein Devices (skipping the pistol, since the Assault Rifle uses the same ammunition and is functionally the same weapon but way better in every way), then the Shotgun. I don't upgrade this skill at all.
4. Repair: Lets you fix weapons that have degraded to the point of being broken, and lets you fix broken vendor terminals. Worthless. If you're using maintain, your weapons shouldn't become broken. It'll let you have access to a shotgun slightly earlier... by like ten minutes. The broken vendor terminals don't have anything special. Yeah... don't put any points into Repair.
5. Research: Mandatory on Deck 3: Hydroponics. Additionally, researching organs typically gives you a moderate damage bonus against the type of enemy that the organ came from. It also gives you access to more powerful healing supplies and some unique implant buffs. If you intend on using Exotic Weapons, research is mandatory since you have to research each of the weapons before you can use them. I typically max this skill by the end of the game for the damage bonuses and healing items.
Weapons
1. Standard: Easily the best weapon class in the game. Gives you access to a handgun, a shotgun, and an assault rifle. The assault rifle is hands-down the undisputable best weapon in the game due to its accuracy, magazine capacity, fire rate, damage per round, and ability to fire anti-personnel and armor-piercing rounds in addition to standard ammunition. There is no threat that the assault rifle can't handle. Prior to getting it, the handgun is basically the same weapon but with a smaller magazine and lower damage - it even uses the same ammunition. The shotgun is kind of crappy, but it's a great disposable weapon since the ammunition is (in SS2 terms) plentiful and the weapon itself is fairly common. I always max this skill ASAP.
2. Energy: These weapons are fairly unimpressive. Their two greatest qualities are infinite ammunition (provided you can get to a recharging station every so often) and bonus damage against mechanical targets. The problem is that mechanical targets aren't very common, and they do reduced damage against organic enemies which are super common. If you have the inventory space to carry it, it might be worth upgrading Energy to 1 and carrying around an Energy Pistol to destroy cameras, eggs, and worms without wasting ammunition. The EMP Rifle is hands-down the best anti-mech weapon in the game, but armor-piercing rounds with the assault rifle are only slightly less powerful. The Laser Rapier is also slightly better than the Wrench, but not enough for it to be worth the investment. I generally don't bother with this skill at all.
3. Heavy: Gives access to the Grenade Launcher, Stasis Gun, and Fusion Cannon. The only weapon of the three worth bothering with is the Grenade Launcher, which is actually a pretty good weapon with fairly common ammunition. Stasis isn't even worth the inventory space, and the Fusion Cannon is pretty much completely overshadowed by the assault rifle since assault rifle ammunition is a hell of a lot easier to come by. If you feel like using the Grenade Launcher, invest a single point into this skill. Anything beyond that will give damage bonuses to the grenades fired... but it's probably not worth the Cybernetic Module investment. I generally don't put any points here, but from time to time the grenade launcher is pretty cool to have.
4. Exotic: The only weapon worth anything in this category is the Crystal Shard. It's essentially a more powerful Wrench that you get mid-way through the game and have to research before it can be used. The rest of the exotic weapons are found really late in the game, aren't particularly useful, have limited ammunition, and require high research skill. I'd never put any points into this since frankly, the Wrench is pretty decent already.
Stats
1. Strength: Increases your inventory space, increases your melee damage, and allows you to wear heavy armor and wield heavy weaponry. Super useful. You need at least 2 points in strength to use the assault rifle and light armor, but more points into this won't hurt. I usually max it by the end of the game.
2. Agility: Increases your movement speed and reduces weapon recoil. I honestly don't find this skill to be particularly worthwhile. To me, it's kind of a dump stat. If I have spare Cybernetic Modules and I've already leveled everything else that I want, then I invest in agility. Otherwise I avoid it. So the amount of points I put into this vary, but it's low priority.
3. Cybernetic Affinity: Reduces the number of ICE Nodes when hacking. It's a quality of life buff worth having if you hack a lot and don't feel like save scumming. If you do save scum, or you don't really care about hacking, it's pretty worthless. I usually put three or four points into it, but it's of pretty low priority.
4. Endurance: Increases your health pool and resistances to environmental hazards. Good to have, but not mandatory. Like agility, I find Endurance to be a dump stat. If you find that the game is difficult and you're taking a lot of damage, go with Endurance first. If you're not taking much damage, go with Agility first. The amount of points I put in this also varies, and it's also low priority to me.
5. Psionic Ability: Increases your energy pool for psionic powers and grants access to higher tier psionic abilities. Completely worthless unless you plan to actually use psionic abilities. I don't like the psionic abilities, so I don't invest anything here.
O/S Upgrades
1. Cyber-Assimilation: Gives you a fairly weak healing item whenever you kill a mechanical enemy (not counting protocol droids, since they aren't lootable). Pretty worthless.
2. Cybernetically Enchanced: Lets you use two implants at the same time, but not two of the same implant. You can potentially get some decent buffs out of this, especially if you have high maintenance (for the increased duration) and/or high research (for the alien implants).
3. Lethal Weapon: 35% damage buff for melee weapons. Pretty much mandatory if you plan to be melee focused, and great if you're looking to save ammunition by using a melee weapon from time to time. Overall it's worthwhile to get.
4. Naturally Able: Gives a one-time bonus of 8 Cybernetic Modules. This one is kind of a waste. It might help you get to a higher level of a useful stat immediately, but in the long-term it'll just mean you have more Cybernetic Modules thrown away into dump stats. Probably not worth it.
5. Pack-Rat: Gives you three more inventory slots. Pretty worthless, unless you really are a complete pack rat and half your inventory is taken up by potted plants and potato chips.
6. Pharmo-Friendly: Gives you 20% more health and PSI points from Hypos. Nice, but not mandatory since healing hypos are pretty common and fairly cheap from vendor terminals. If you're playing a PSI character though this one is practically mandatory given how many PSI hypos you'll be using over the course of the game.
7. Power PSI: Eliminates burn-out damage from Psionic abilities. Worthless to non-PSI characters, fairly worthless to PSI characters with a high PSI skill. Generally not worth it to anyone.
8. Replicator Expert: 20% discount on vendor items. Great when paired with Hacking to get cheap items, but still only useful if you actually buy lots of items and have money trouble. If those aren't really issues, this is worthless.
9. Security Expert: +2 Hacking for the purposes of hacking security cameras. Worthless if you're already investing in Hacking and Cyber-Affinity, which you should be.
10. Sharpshooter: 15% damage bonus with firearms. Absolutely badass if you're planning on mowing people down with an assault rifle. Useful to any character planning to use guns, though.
11. Smasher: Gives you an overhand swing with melee weapons for increased damage. Great when paired with Lethal Weapon for melee characters, though Lethal Weapon on its own is a bigger damage increase than Smasher is. The exception to the rule is the Crystal Shard from Exotic Weapons though... Smasher doubles the damage it deals, making it the strongest melee weapon in the game (deals slightly more than three times as much damage per-swing as the Wrench with Smasher).
12. Spatially Aware: Fills out the maps on the Von Braun (but not the Rickenbacker). Pretty worthless.
13. Speedy: 15% movement speed bonus. More of a quality of life perk than anything else. Might be useful to melee characters or character that don't invest much in Agility, but it'd be only marginally useful at best.
14. Strong Metabolism: 25% damage reduction from toxins and radiation. Nice to have, but not really mandatory since there are hypos to cleanse those effects, and environmental suit to resist it, and a PSI ability to resist it. There are worse places to put an O/S point.
15. Tank: +5 health. Worthless on the lower difficulties, potentially very useful on Impossible since that difficulty has such a tiny health pool.
16. Tinker: Reduces the cost of modifying weapons by 50%. Completely worthless, since Modify is completely worthless.
Hope that helps with your character building!
