The difference is that 3Es skill system was more open, especially skills like knowledge and craft which were further divided into several categories. Also 4Es automatic skill gain doesn't lend itself very well to using skills for role playing purposes as, according to their skills, a 4E character can basically do everything.
More than in 3E, skills in 4E are just another level dependant ability.
As one who has definitely approved of the changes, I can tell you why the decision was made. Everyone took the skills that allowed you to survive and thrive as an adventurer. That's what the consolidated skill list is, the skills which allow you to deal with the various story elements that the DM is going to throw at you. If you don't have someone in the party that can climb a wall, open a locked door, or has the knowledge skill necessary to solve a puzzle, it can bring the game to a screeching halt over something trivial. Now a party is generally able to have all the skills they need to generally traverse routine obstacles in a dungeon, and a few can do it well enough to beat the difficult challenges of that skill. It doesn't bother me like it does you, because I don't see it as heroes being able to do "everything" but rather heroes gaining more and more experience in adventuring and having the general skills to do that.
I also don't mourn the loss of profession and craft skills from 3.5. It is nice if you have a skill that allows you to forge your own swords, but after a couple years everyone quickly realized that it was a skill that became useless after level 5, and it didn't help you to traverse Castle Maure. Profession skills generally didn't have much to do with the wider game, and only provided a pittance of income. It allowed you to mark "Smith" or "Basket Weaver" on your character sheet, but it didn't do much else than that. If I want an ability worth putting on my character sheet, I want it to be useful, and if it is of less utility than other abilities I don't want them competing for skill points with the more useful skills that will keep me alive in day to day dungeon crawling.
I do get what you are saying though in that there is a loss of specialization. With the Open Locks, Disable Device, and Pick Pockets skills combined into one "Theivery" skill, all rogues have a general proficiency in "roguishness" but there is no specialization in being a cutpurse, a safecracker, or a troubleshooter respectively. However, I don't think it is worth tearing down the general skill list which allows people to handle the mundane aspects of dungeon crawling. I think you still want the party to be able to handle the obstacles which require a rogue's skillset.
This is what my talents system is trying to accomplish. Keep the general proficiency to handle whatever the DM may throw at you, but add a rather superfluous layer over top that allows you to specialize within a skill or grab a ritual-like ability. So a wizard well versed in creatures of the shadowfell has "umbral lore" as a talent can still know enough of general creatures of the planes to have a chance of meeting the DC's for necessary knowledge checks with his arcana skill, but identifying creatures of the shadow plane in particular comes easily to him.
So not only will a talent system bring back the specialization of the wider 3e skill set, I'm bring back 2e Non-Weapon Proficiencies baby! Now that's specialized skills!
This I don't get at all. The mechanics for resolving a skill check are exactly the same in this edition as the last edition.And I don't feel that there was such a big combat/out of combat split in 3E.
Most things you could do in 3E during combat also made sense when seeing through "non combat lenses". The only thing really striking out is falling, and that is a problem in every D&D edition.
In 4E on the other hand there is a big rift between how the game world is percieved during combat and outside of combat. That includes for example the different geometry (1-1-1), mechanics linked to having a certain number of combats a day without any regard to what happened in those combats/how long they are (milestones) or having abilities which only trigger when used on level appropriate enemies, but not when used on enemies which are too weak.
I think you might be a little nitpicky here. For example, the way you fight doesn't work fundamentally differently if you're fighting a colossal creature vs. a medium creature for example in either 4e or 3e, and you don't really worry much about that. That's a much more obtrusive suspension of disbelief than getting an extra action after two encounters.
But yeah, having daily, at will, and encounter abilities is all about narration, not simulation. Either you are on board with that, or you're not. Come to think of it, having daily, encounter, and at-will non-combat abilities might be a way to make skill challenges more cinematic as well.