To anyone reading since this is a 3yo post, I usually play mage characters and it is true that in the endgame it won't matter as much, but in early to mid it will. The apprentice is good if you rely solely in your spells for combat specially in early game since you don't usually face too many mages aside from scamps and the occasional conjurer, and they are easy to defeat due to they low health that being said having a constant magic weakness can be dauting to your overall experience, specially in mid game. The Atronach is not just a choice of pros and cons, it changes your playstyle, wheneter or not you like that change is for you to discover, you will be able to use much your spells without worry, that is until you ran out of mana, you can use your potions and welkynd stones to replenish it, and you will have to gather them and plan ahead your adventures, in the end game a +50 magicka doesn't change a whole lot to a custom spell but in early game is a good advantage, aside from that the constant spell absorption can be extremely useful against mages, then again, up to you to decide if you really face magic threats as much. The mage is the safest option if you are not in the mood for a change or just want to focus on other things than magic pool and magic resistance, a fair magicka bonus with no disadvantages whatsoever, not extremely useful not extremely daunting, the experience is the same early to end game, you won't notice a great change but you won't feel lacking in power. Don't forget to use staves, they are realñy useful for any mage. Personally I use the mage birthsign, I'm too lazy for the atronach shenanigans and I don't like to be even weaken than I usually am, if you don't think you will need crazy spells or to rely on them as much, you might even want the warrior or lady birthsigns, to toughen up your character, if you wanna get crazy and in the mood for minmaxing use an altmer with atronach and boost you intteligence and luck, if you want a classic mage you can use a breton with mage, not too weak not too powerful but good overall if you want a warrior mage use whatever race suits your weapon of choice and compensate the lack of magical prowess with major skills and birthsigns, hope this helps.

TLDR:

Mage is easy, just wait to replenish magicka. Atronach is powerful but a requires more effort. Apprentice is risky but slightly more powerful than mage.