Okay normally I don't wind up playing mages.

What I am looking at is a pure squishy mage...dash of stealth This is the basics for what I'm looking at.

Breton (for abilities and looks)

Stones: Mage Stone (at first, then Lady stone for health/stamina regen)

Key Skills:

Destruction (key damage dealing ability, not going for the specialized perks like disintegration due to quirks with them)

Restoration (heals, some dawnguard combat spells)

Alteration (using the skin spells for defense, and utility spells)

Illusion (frenzy, invisibility, muffle, light spells. Key being quiet casting)

Conjuration (zombies, familiars, daedra summons as needed for backup)

Enchantment (only for enchanting personal gear, some money making; mostly mana regeneration with some resists/other)

Sneak (cautious exploration, not rushing in slinging spells)

Optional:

Smithing (for jewelry to enchant for coins, more a tinker than a blacksmith)

Alchemy (mostly for utility potions: health/magicka restoration, invisibility + healing, cure disease)

Lockpick (since I haven't found a unlock spell mod I like yet)

Basic personality: Like many bretons born to common group, out looking for a way to boost their standing and power

Guilds/Factions - ALL!

Companions - Learning the ways of the warrior, and building up honorable reputation and experience working with physical combatants (will not stay werewolf)

Dark Brotherhood - Best way to learn about killing, is to kill... and gain the experience and contacts needed to be very powerful in the shadows

Thieves Guild - Much like the Dark Brotherhood, a way to gain experience and contacts that can assist in a variety of ways

College of Winterhold - Best place in Skyrim to learn the ways of magic

Stormcloak Rebellion /Imperial Legion - Undecided on side, but in many ways both sides have strong arguments for the mage's aid in the war (saving that for later)

Blades - Right up till given the ultimatum to kill the dragon... at which point the realization that the old blades are no more all that's left is a weak watered down ghost with nothing but vengeance and frustration left to them

Side quests - All

Like most bretons they will see those little quests as ways to hone skills, build experience and reputation... all of which add up to personal power and glory.

side quests of note:

Forsworn Conspiracy - try for both side(aka get the forsworn gear then kill the leader), else pure forsworn due to dislike of the nords involved (and to have a way in to the forsworn as allies)

Now end game I may swap out to heavy armor (with shield) but for the most part thinking pure clothe wearer

You're kind of spreading yourself thin, there. That's a lot of skills and a lot of factions, and not a lot of focus. If you're going to use Destruction, I'd narrow it down to one "elemental" type of damage, either fire or electrical. I'd either go with Restoration or Alchemy--in the case of a "pure" mage, I'd go Restoration, as the anti-undead spells are useful for your purposes. Most of what you'd use Alchemy for--healing, invisibility, etc.--can be duplicated by other magic schools. I'd either be a Conjurer (summoning daedra) or a Necromancer (raising undead), not both. If you're only going to use Smithing as a money-maker, you really won't need to put any perks there. I wouldn't bother perking Lockpicking, either; the skill will level on its own if you use it enough.

From your faction choices, it really seems you want to be a jack of all trades rather than a pure mage. If your main damage-dealer is Destruction, why bother with the Companions? Why learn "the ways of the warrior" if you aren't one--and would they really want someone around who disdained edged weapons in favor of spells?

If you're looking for a "squishy mage with a dash of stealth," might I recommend a Conjurer/Illusionist? Sneak through dungeons/lairs turning the inhabitants against each other and use a summons (or raise a dead enemy) to mop up. I've done this using: Conjuration (this might give you more room to be a summoner as well as a necromancer, as you probably won't need to use the Bound spells at all), Illusion (of course), Alteration, Restoration and Enchanting. It's still a "pure" mage, in that it relies solely on magic skills except for sneaking, and even that is dependent on being skilled with Illusion, not putting perks in the Sneak skill itself. It's pretty amenable to a lot of questlines: the College of Winterhold, the Thieves Guild, the Dark Brotherhood, the main quest (the easiest time I've had going through the MQ was with my Conjurer/Illusionist), the Civil War. Not so much the Companions, though! When I did it, I was able to avoid leveling Destruction at all, although you could always use that as a fall-back damage-dealer.

Well I know it's a thin build, but the aim is to master all magic.

It's not so much learning the ways of the warrior, so much as joining them for the purpose of working with warriors (aka learning mixed unit tactics, but metagame they have some of the better tanks in the companions and some very well paying missions to kill dragons)

It's much like how they are going to wind up part of the dawnguard, even though the dawnguard has no mages really...

Also for a pure mage you might consider an Altmer, they're arguably the best for pure mags.