Like what? Apart from better graphics and different combat? They've removed skills, weapons and abilites since Morrowind.
And added a lot more. A lot of what was removed since Morrowind really is small, needless redundancy.
Skills removed and not replaced: Medium Armor, Acrobatics, Athletics, Spears
That's really it. Every other skill from Morrowind exists in Skyrim in some fashion, albeit there are different takes on the skills, yes.
*Armorer - removed and replaced with Smithing. I find this to be a huge upgrade, and adding more complexity than Armorer ever offered.
*Hand to Hand - still in the game, although not as a skill, but there are specializations in hand to hand allowing it to be a playstyle.
*Unarmored - not in the game as a skill, but offered as a specialization within the Alteration skill tree.
*Mysticism - not offered as a skill in the game, but most of what it did is in the game, just in different schools.
*Long Blade / Short Blade / Axe / Blunt - replaced with One Handed / Two Handed, and specializations within each skill tree.
*Mercantile - has simply been merged with the Speechcraft skill
*Pickpocket - was never in Morrowind, made a return.
*Enchanting - removed as a skill in Oblivion, returned as a skill in Skyrim.
That doesn't scream mass removal to me, and in many ways it sounds like more than we had before.
The skills themselves now offer
more customization than before, because the skills aren't just a generic 1-100 rise, but now the perk trees offer specialization within each skill. Thus a level 100 in Conjuration character could be completely different than a level 100 in Conjuration in Morrowind or Oblivion. You now choose a specialization - summoned Daedra, necromancy, or bound weapons - or any of the possibilities. These specializations exist for virtually every skill: Destruction - frost, fire, shock; Conjuration - Daedric summons, necromancy, bound weapons; One Handed - axes, maces, blades, dual wield; Two Handed - battleaxes, warhammers, greatswords; Sneak - stealth damage, or silent movement; Speechcraft - mercantile / haggling or NPC interaction; Smithing - light armors and weapons, or heavy armors and weapons; etc...
That sounds like more complexity to me.
The spellcasting system I feel has been greatly improved. We have lost some effects, and I think that svcks, but I think what we got is far better than a few effects that we lost. Spells can now be cast in many different ways than just the simplistic "target", "touch", "self" effects, allowing for new styles of mage play that was never possible before. I don't think the potential was fully realized, but I do believe what we have is better than the old system with Spellmaking.
What I see in Skyrim is deeper, more complex skills than before, deeper, more complex combat and magic than before, with only minimal losses that we've had before that don't come anywhere close to outweighing what we've gotten.