Skyrim got me thinking of Morrowind again and after not playing it for I'm not sure how many years it once again inhabits my hard drive and has undergone the Morrowind Overhaul mod.

It looks frankly awesome, but I was reminded of its one flaw in my opinion. ... the leveling system.

I looked at a few guides but they were conflicting and of dubious quality, so my basic question is this. I recall you don't want your 'real' major skills to be the skills you use the most due to the fast leveling causing you to loose a lot of stat points.

What I was thinking of was playing a mostly pure mage, so what would be the better break down for major and minor skills? I used to know all this, I even played a character at one point who's goal was to never use a weapon in game (outside of the ending where you had to), but that knowledge has apparently drained out of my head.

Maybe you're thinking of Oblivion, because in Morrowind it's a safe bet to have the skills you'll be using set as your Major/Minor skills.
Except Athletics... it's rather pointless to pick because it levels quickly no matter what.

Here's my take on your first statement and I'm sure I'm not alone in this view. The problem is, if you want to be strong in a particular skill at lower levels, you need to take it as a misc skill so you can train or twink it more than 5-10 times in one level. To illustrate, lets say you wanted to be a strong conjuration caster as soon as possible (level 1-5 or so); you could take conj as a major but now even if you devote all of your leveling skills to conj you can still only increase 10 max points each level. Let's say I want to get to 80-90 conj really fast. I would take it as a misc skill, and once I had some cash train it like 30 times a level - once again this is only possible if the skill is outside your leveling skills (a misc skill).

I pick majors and minors according to the following thinking: majors are for very useful skills that are a pain to increase by non-training, and that I can accept raising only at a moderate rate (examples: enchant, speechcraft, athletics, sneak); minors are for generally useless skills that a bonus to would help in the early game (examples: merchantile, security, weapons you don't favor). I also try to have every stat represented among the 10 major/minors as balanced as possible (i.e. 2 strength skills, 2 int skills, 2 pers skills, maybe 1 speed skill, etc). Lastly, I never ever put armor skills in the major/minors - they are just too easy to increase by letting yourself be hit repeatedly.

During play, I keep a sheet of paper nearby and the beginning of each level, I write down the current skill number for all skills I plan to use for the attributes I plan to increase so I can track what skills need use/training to get the 5x multiplier.

In my current playthrough I made a restoration specialist who I fancy as an imperial cult fanatic (i.e. first loyalty is to the Nine Divines always). Custom class of course - here's the breakdown of what I went with and why. Maybe it will help you to decide for your character. I'm level 13 now and doing the "get named horator" part of the main quest and after I finish writing this I'm gonna play some more. After all the years I have played morrowind the farthest I have ever gotten is to finish the main quest - I still have never done tribunal or bloodmoon because I always feel like I can make a more fun character. We'll see if I stick with this one.

Race: Breton (50% magic resistance and mana pool multiplier, plus I love the voice which apparently most people hate - and I'm using boots of blinding speed)
Sign: Atronach (50 spell absorption and I personally believe if you rest to regain magicka you are doing something wrong - there's a zillion easy ways to absorb free magicka)
Specialization: Magic (to get the most out of per-cast magic skill increases and to boost unarmored increases)

Majors:

Restoration - Start with a 40 giving me Hearth Heal, a spell useful through the whole game. With a modest score in this one I can (and did) get fortify skill and fortify attribute and then spellcraft up some custom spells which when cast quickly in series allow me to boost up any attribute or skill to obscene levels for short amounts of time. Some spells I made include an enchant/INT booster that allows me to enchant my own items (unlimited cast on use and up to 110 points of constant effect), a 3 minute boost to blunt weapon and restore health 4, a 3 second illusion skill booster that allows me to cast the best standard invisibility and chameleon spells.

Enchant - One of the most difficult to increase skills in the game, even when you recharge and make your own items.

Speechcraft - Painful to increase and so important for those early quests.

Sneak - Not too hard to increase but you have to go do something else for an hour or so - even so this one is easy to control so you dont level too fast.

Athletics - Can be annoying as it continously increases as you run around, but I run everywhere and I still only have a 43 in this at level 13 (started at 30).


Minors:

Axe - this character favors blunt weapons as an imperial cultist so axe is a no-brainer for use with summon bound axe for a devastating early-levels weapon.

Spear - a training skill for endurance purposes. First 12 levels had endurance as one of the improving stats for obvious reasons, using only spear and heavy armor. If it isnt obvious, consider that your hit point gain per level is (endurance/10) [retain fraction for next level]. If you don't increase your endurance right away you are getting about half the hit points you could be getting.

Hand-to-Hand - I'm not really into this skill, placed here because it's basically useless to me.

Security - You can make a Open 100 enchanted item using an extravagant shirt (easily obtainable) either yourself or pay only I think about 10-20k septims. In the meantime a 15 in security is plenty for most early locks you will face.

Mercantile - in my opinion getting all the money you need is very easy. Meanwhile a 15 at game start isn't bad to help you along the way.


Now a quick total shows I have 1 STR, 2 INT, 1 WIS, 1 END, 1 AGI, 2 SPD, and 2 PERS skills. Now let me say which skills I consider really important for this character (skills I want at 80-100 ASAP) - unarmored, blunt weapon, conjuration (for summonings and command), alchemy. Note that none of these skills are in the leveling skills with the intention of overtraining them. Hope this helps and I'm off to play MW!