I'm Level 50 and playing the good guy (for whatever that's worth in a Bethesda game). I'm not too keen on the guilds at this point because:

a. The Companion quests were buggy beyond belief, I had to spoil myself on the entire quest line before completing them so I could figure out what console commands to use.
b. I became archmage in the last "guild" I joined, which is laughable considering my character can't cast anything beyond Novice.
c. The early thieves guild quests are just petty thievery and shakedowns with no "good" options. Not to mention they're beneath my Level 50 character.

So I'm planning on skipping the Thieves Guild quests with the assumption the only rewards will be the usual (become leader, get some spanking new armor and a room to store stuff). More importantly, will I miss any other quest lines later on?

Nah, besides Nightingale Armor, the Skeleton Key (you have 600+ lockpicks by now right?! ), 7 fences with 4000 septims for barter every 2 days, or the ability to use 3 extra divine powers, you're not missing anything. Each of these guild rewards can be replaced with something else in the game: Lucan Valerius for 7 fences, Invisiblity, Absorb Health or Frenzy for the 3 greater powers and your own enchantments are always more powerful than quest rewards (Nightingale) in Skyrim.

As for quests, as far as I'm aware they don't overlap with any others.

Are you skilled at sneaking etc? I found it impossible to complete the thieves guild quests without killing people. Heaps of people. Dozens of people.

As a member of the Dark Brotherhood and a member of the Thieve's Guild I don't see the problem with slaughtering dozens. LOL

Which version of the game were you playing(1.0, 1.1, 1.1, 1.2, 1.3)? The Companion quest line was flawless for me and I'm playing on version 1.1.

Neither did i, but the OP said he was playing the 'good' guy...

i seem to be alone in thinking this, but i happen to think the thieves guild questline is one of the best in the game and has one of the most interesting npc's in the game too. Also, i think it has a lot more depth to it than the other guild quests and it's equivalent in Oblivion. But that's just me.

I really loved the Thieves guild, too. The story is the best of all guilds IMO. Without spoiling anything I can tell you that it's about revenge and involves daedra so it's not really a "nice guy's path", but it's absolutely worth it even just for the storyline, the rewards are just icing on the cake. I actually rerolled my assassin character just to play through it again ^^.

No. They treat you like [censored] even if you are the guildmaster.

nightangale armour is the coolest in the game, really suits stealth characters

I would recommend it because it's really fun and only becomes slightly monotonous towards the end.

I'm note really sure why you would bother asking the question if you are already so dismissive of the idea. If you're against stealing things, it sounds like you've already made up your mind.

I'm about halfway through them myself and they're great fun. But yeah, you can't be a "good" thief. In the end, it's a guild of thieves... big surprise.

Sounds like you've already made up your mind and this was a pointless question, though really, not doing it because some other guild quests bugged? May as well stop playing the entire game right now, you WILL find bugs. But I'll answer anyways, the thieves guild is the only guild that has any fleshing out, it is by far the longest and most indepth of the guilds.

I'd reccomend doing it although the special guild quests are only a waste of time. Good to get more shops in the ratway but to me it's a waste of time.

If you want to be good, no. This isn't like Oblivion where you can at least justify it by being Robin Hood and giving to the poor. In Skyrim, you steal stuff that doesn't belong to you from people who are nice and don't deserve it.

If you don't mind that, do it, but do ALL of it, not just the main Thieves' Guild questline, or else it's disappointing.

Yes, I encountered no bugs as far as the Thieves guild went. 1.2