the only thing I know is that the Skyrim I play now looks really nice and runs very smooth. That's good enough for me. And those things mentioned is not been completely patched yet, so I guess it is what they intended... There are also several other little bugs cosmetic fixes the community have cleared up.

I think "the way they intended it" is a bit of an inaccurate statement. The developers probably intend a lot of things that don't make it into the game. The only reason I avoid modding myself is that I'm paranoid it will mess up cheevments for me.

Minor pet peeve: if an MMO allows UI modding, then the developers intended people to use that. The reason UI mods are so prevalent in certain games is because the developers intentionally allowed access to that particular part of the code. That said, MMO UIs are usually pretty good these days. I haven't installed a mod in an MMO in years.

I usually play through at least once the vanilla version before I apply mods and honestly.... most mods don't manage to feel like they should be in the base game. However, there are mods that I consider "essential" by now, as they do improve the game overall and make my live easier.

Better Dialogue Controls - sometimes the game loses fokus on the dialog and you pick a choice you didn't wanted - not anymore.
Localized Thieves Guild Jobs - ask Delvin and Vex about jobs in city XY, get the quest, done. No more save / reload until I get corresponding jobs where I'm heading.
Unknown Enchants - seeing if I already know that enchantment or not on the item itself? Yes please.
Acquisitive Soul Gems - no more Black Soul gems filled with petty souls. Souls check for a gem their size or don't get "caught".

When Vampires attack - I hate Dawnquard for killing NPCs in town. Which is why I usually do it first. With this mod citiziens don't try to be a hero and run to safety, while guards / companions / vigilants of Stendaar will stand and fight. Doesn't make NPCs invulnerable so it doesn't always work, but when I see a complete Khajiit caravan run from their place near the stables towards Whiterun too busy to talk, I know what's happening.
Run for your lives - same goal as the above When Vampires attack, only with Dragons.

Adopting children with Heartfire. Yeah. Not a feature I was looking for. At least I long thought so. Then I found out about KhajiitChild Maisha..... how can you not fall in love with that little brat?

Faster Mining - changes the striking animation when mining from 9 to 3 - timesaver.
Interesting NPCs - just what it's called.
Khajiit speak - absolutely fantastic immersion-wise when playing Khajiit.
Talking with Septimus Signus while looking for the Elder Scroll:
- Pay attention, yes? Khajiit will ask you a question. Now... where is the Scroll?
- Khajiit does not want to hurt you. No, that is a lie. Where. Is. The. Scroll?
Or with Farengar, the mage in Whiterun:
- The thinner the patience of a Khajiit wears, the sharper their claws become, no?
- Your tone is becoming irksome, mage, but Khajiit will ask anyway: What next?

cheers

A few lines down, I stated that I do understand that someone might not like modifications, even unofficial patches. It's just the statement "out of respect for the authors' work" that irritated me.
But whatever... I'm not sure why I wrote that post, it will at best drag on for a while with noone changing his mind (probably this syndrome: http://xkcd.com/386/).

Well I don't know why it would irritate you?

There's always a few mods that I haven't checked out / discovered and that I'd consider great afterwards - like the mentioned Interesting NPCs.

But it's seldom that a mod flat out stuns me. Which just happened with Vilja in Skyrim in combination with a multi follower mod...
Just bought my home in Whiterun and went to drop of some stuff. Vilja starts a minute long conversation with Lydia (yes, that Lydia) about.... diets. Basically Vilja asking for a diet to eat as many sweetrolls as possible and how much she's starving with Lydia pulling a joke on her.

Anybody still seeing a (modded) Skyrim as generic with the depth of a puddle, needs to get a reality check.

Edit: yesterday I managed to catch a sweet spot and gotten some recorded. Mind you, this is nothing quest oriented, just random chatter depending on your companions. Other companions, other chatter. But it really makes you stop doing what ever you wanted, just to listen to it.
Random chatter part 1, random chatter part 2