Whole new perk system, entire new crafting skill... bound to be some growing pains.
With the exception of how stupidly easy it is to cap Smithing and Enchanting, I actually like the new perk system and crafting system if I have to be honest.
The perk system stops people being the master of the universe in every skill, which you could be in Oblivion let's not forget. Mages are Mages, Warriors are Warriors and Theives are Theives, you can make hybrids as well and so you can tailor your character to however you want but you can't master everything. But of course there are some issues with the perk system, like the fact I just don't think melee weapons should be divided as skills anymore, it doesn't really make much sense to me that I have mastered one-handed swords but yet hit for less damage with a greatsword then a skeever deals with it's bad breath. I think their should be a few perks that separates 1 and 2 handed weapons but not skill. A lot of spell tree perks are useless or become useless later on (what perks in one-hand become useless? none?), more so the skill level perks since enchanting makes spells free and thus what's the point in having say the Master Destruction perk?
The new crafting systems are not over-complicated for what it's meant to be and the items required for it. The only real issue is that the following 3 effects exist in the game that should either have been very toned down or non-existent, Fortify Smithing, Fortify Alchemy and Fortify Enchantment. As for the new alchemy system could have been an improvement if the only change was that you selected the type of potion you wanted to make but more has changed then that, where have named potions gone?
One thing I would like the return of is attributes, I don't think the way Oblivion did attributes was at all well thought out back then either but I don't think their removal has been beneficial to the game play since now all the races are almost identical minus a once-a-day ability, some resistance effect, height and weight. I think the return of attributes which are based off of your skills (in other words they level in a similar way in which you gain character levels) but also with racial modifiers would have made the races a bit more unique then they're in Skyrim, possible more unique then they were in Oblivion.