I voted fallout because well, that system is not completely broken (although still easily abused). However I do not think that Bethesda should use a fallout style level up system in Skyrim, they should adapt and balance the current TES system.
Here is how I would do it(apologies for possible incoming ramblings):
Keep the 'leveling up major skills raises your level' system but,
have four tiers of skills rather than two, so say rather than major and minor (or major,minor and misc in Morrowind) have for example prime,major,minor,misc. Have the player choose just a few skills for prime major and minor and then the rest are misc. Prime skills cap at 100 major skills cap at 75 minor skills cap at 50 and misc skills cap at 25. Keep the mastery bonuses from Oblivion but make them a bigger deal so that what skills you pick really matters, your character can use all skills atleast basically but can only really master a few forcing you to specialise but still allowing for the freedom of skill use which is a hallmark of the elder scrolls series.
Lastly but most importantly overhaul the stupid stat system. Make Luck useful again and make personality worth a damn. There should be a fixed number of attribute points to spend at every level up giving players freedom to simply play the game and use their characters main skills freely without gimping themselves at all. However this fixed number of attribute points should be relatively low, again meaning you have to specialise and cannot max everything. Oh ye one last thing,skills should raise slowly meaning you level at a relatively slow pace, imo you level far too fast in Morrowind and Oblivion, basically having a god character before you have even seen half the content.