Trevor, my second character after having spent 109 hours playing as a High Elf, is an Argonian thief, who also likes to pull out the two-handed greatsword when up close and personal.

I'm level 7 and I've put points into Sneak, Light Armor, Archery and Two-Handed. However, I am unsure as to what other skills I should look to invest perk points into in the long run. Any suggestions?

This is weird ... I'm at level 51 in a Sneak/Archery/Thief playthrough.

I would urge you to cocentrate on two skill trees in particular: Sneak and Archery

The Perks in those two trees are incredible ... I have 95 Sneak and can even walk and run without being detected. I aslo never set off any floor-based traps and am basically undetectable. I get critical hits on enemies that I'm crouching beside!! Build up your Sneak Tree.

Archery: I have 100 Archery Skill, can slow time 50% while zoomed with a bow, can zoom in with a bow, I do 100% extra damage with a bow ... and get this .... I get 3 times the normal damage for a sneak attack with a bow. I stagger enemies 50% of the time with all arrows.

I also put points into Smithing, to craft Dragon Armor and am quite good at Heavy Armor and Alchemy.

Basically, I go nearly everywhere undetected and kill nearly everything from the shadows. No one hears me and no one hardly ever sees me. It's tremendous fun.

Well, the OP was asking how to work with 2H. But your advice is valid.

OP: Don't spread out your perks amongst trees, chose 2-3 and specialize. Having ONE point in any weapon or armor perk tree is fine, as the 20% boost you get with the first point is a big jump. But only continue to perk the skills you want this character to use the most - in your case, sneak, archery and 2H. One point in light armor should be all you need - you don't plan on getting into toe-to-toe situations much.

My 2c.

Edit: Yeah, we need a Devo hat mod!

If you are playing on Expert/Master. Try to get your smithing skill up even if you dont spend points in it, and then use something like Leather Armour and keep improving it.
My thief character was Sneak, Pickpocket and One Handed. By level 20 or so (fast) I really regretted not putting anything into armour, and I got absolutely slaughtered by everything.

Its a shame that putting points into something like Pickpocket really gimps you, and lockpicking? Kind of useless tree all together.

Anyway, if your going archery (I barely touched it) it probably wont be an issue for you.

PS, that char is level 49 now and nothing is a threat anymore. So it scales very strangely.

I would spend 3 points in the Sneak tree, up to the perk that gives you 3x sneak damage with bows, 8 points in Archery so you can get the 100% damage bonus+ 50% slow time while zooming and 7 points in two handed so you can get the 100% damage bonus+ 25% reduction for power attacks and the beheading perk (you don't need to take the last one, but its immensely satisfying to cut someone's head off).

Aside from that, go buck wild on the perks you want to play around with and you'll do fine. As far as your armor perks go, they're wasted if you spend any time at all focusing your crafting skills. You can easily get the max armor rating through alchemy and enchanting. I'd recommend you go the heavy armor route with smithing, even if you intend on focusing on light armor. The last perk in heavy armor crafting is the same as the last perk in light armor crafting except you get the added benefit of being able to craft daedric weapons while smithing your dragonscale to the highest levels.

The Assasin's blade perk in sneak is so very, very fun. So is the pickpocket perk that lets you drop poisons into peoples inventory. That one is really complemented by Alchemy, though. The light armor perks are nice but keep in mind that several of them require you to wear all light armor. This might keep you from fully benefiting from some of the dragon preist masks. Just something to consider.
You don't need to follow every perk tree that benefits you all the way to the end. Spend points until you get the really cool perks. Sometimes the rest of the tree is pointless.

Indeed. For some skills, it's not a bad idea to just keep buying multiple levels in the "base perk" as you skill goes up, and ignore the rest of the tree (depending on how you want to use the skill).

Sneak and archery do go together well, but don't write off two handed and light armor (or in my case, heavy armor plus Steed Stone) - being able to move fast and kill most foes with one blow is quite nice. Add sneak to the mix and it just gets so much better. Being able to get close to a group of badguys, pounce on one and take them out with mighty chop, and then actually hold your own in the resulting melee is quite fun. Worked nicely for Conan, after all. (If you also max out your "Freeze Time" shout, this can be absurdly effective. "Scout, shout, and out" is my SOP for clearing rooms with multiple foes. Often I kill them all before they can get weapons fully drawn.)
And yeah, I'm also playing an argonian. I don't consider myself a thief, though, and I think Aliea would be very offended at the classification of archery / light armor / archery as "thief skills". A thief is just somebody who steal stuff, and you can do that with pretty much any skill set.

My 2-handed character likes a combo of sneak roll plus charge attacks. The sneak roll counts as charging. Yeah, the charge attack doesn't really do as much extra damage as it should, but it's fun. There's something awesomely absurd about ninja-rolling into someone and one-shotting them with a hammer.

Thank you very much to everyone for the awesome advice. I pretty much ruined my last game by pumping my Enchanting skill up to 100, and making Destruction and Conjuration cost zero magicka to cast, which just made the game super-easy. I am thoroughly enjoying my re-roll as an Argonian archer, who also likes to whip out the ol' two-handed battleaxe when the going gets tough!