The Morrowind/Oblivion class system was flawed. People don't want to be stuck with only the skills they choose in their class (major skills) and want the freedom to improve their minor skills as they want. Thus players will improve their power rating by increasing minor skills. As a result, player level should increase when you level any skills or else the challenges you face won't be adapted to your power rating anymore.
So first change to do is to make you level when you increase any skill and not just the major from your class.
Then the second flaw in Oblivion. Every 10 increases in a stat you get a x5. Every 10 increases in a major skill you get a level up. As a result, you need to level 20 times minor skills and 10 times a major skill to get the max possible x5 multipliers. The system actually made much much much stronger classes that increases twice as many minor skills as their major skills. Leveling attributes is VERY important, mostly for END, STR, and INT (max HP, carry capacity and max MP). Everyone needs a lot of HP so the strongest mages tended to have very high skills in armorer (cause cloth using mages got a lot of stuff to repair right?), block (cause blocking with a staff works sooo well, well at least it gives you stuff to repair if you somehow get your armorer to 50) and heavy armor cause the mages with the best armor in the game are those that need the most HP right? And since HP gain isn't retroactive, you'd tend to get low level mages with ultra high armorer/block/heavy armor skills long before they level their magic skills.
Second change : attributes are out.
Third flaw which is kinda the direct oposite of the first. Since players that increase 2 minor skills for every 1 major skills are SO much stronger than players that play their class as it was meant to be, game balance is thrown out the window. Is the level 10 world difficulty tuned up for a min-max perfect x5 powergamer that leveled Destruction magic to 100 at level 1 before even starting playing the game or for some casual player that chose the Bard class and went to a speechcraft spree in between making 200 pots of restore stamina after raiding the local farms?
Third change : all skills cause level ups, major and minors in a way that rewards more specialisation. A player that got all 18 skills from 5 to 10 will surelly not be as strong as a player that got both one weapon and one armor skill to 50. From this comes the idea that leveling a skill from 49 to 50 fills up the bar to next level up much more than a 5 to 6 increase.
The system they propose is great. It's exactly like Oblivion except that all skills are major skills really
The only "weak" part of it is the HP/Magika/Stamina level ups where you pick by hand what you want. I don't think it's too bad since linking them to some skills could force people to level skills they do not want to use just for the effects on the stats. Or you could create a skill which direct effect is to increase your max HP? But it would be a pain to define how that skill levels like most "passive" skills in Oblivion (Athletics anyone?) Choosing at each level up a HP or Magika or Stamina bonus is fine I guess.