I mean, yes? That's the design of the class: they get spells that enhance their other abilities. And if you want an especially sneaky ranger, you have Gloomstalker, who become invisible in darkness. I could easily say, "Why should rangers have spells? That doesn't really make sense." But if you weaken the ranger's spellcasting ability, you're blowing a big hole in the class.
Well, ok, then you no longer have the perceived problem that wizards have no way to be as good at arcana as rogues who pick arcana, etc. Right? Why also mess with expertise itself?
A lot of those are a stretch and/or the classes you mention have features that enhance their abilities in those kinds of things that aren't bonuses to skill checks. Monks have slow fall and increased speed, for example; barbarians have advantage on strength checks while raging; warlocks and sorcerers (and wizards) have the friends cantrip and various spells with charm and fear effects; warlocks also have access to Mask of Many Faces; Clerics have Zone of Truth; wizards have divination spells; Barbarians already have Danger Sense (as you yourself pointed out).
Look, if you are going to redesign the classes from the ground up because you think there should be a tight connection between skill bonuses and the fiction, more power to you. But it's not fair to the rogue to single them out for their access to higher skill bonuses compared to other classes when other classes have different ways to get at similar results. And, you know what, any class is free to take a level of rogue for expertise if they think it's that great! It doesn't mean they have to become a scoundrel; it just means they're focusing on their skills at the expense of progressing in their other features.
So let's think about the tradeoffs here compared to the expertise feature. On the plus side for the rogue, they can gain expertise in any skill check -- not just those they picked for their character -- if they have the time to analyze the situation. One down side is they can no longer be experts at hiding in combat, which is pretty rough for certain builds, who basically require they be able to hide nearly at will, at least when the terrain supports it. Rogues can no longer be experts in acrobatics really, either, but you gave them the ability to make acrobatics checks as a bonus action, so I'm ok with that. Certain subclasses have features that allow them to do certain things using skill checks in combat: The Inquisitive's Insightful Fighting, the Swashbuckler's Panache, the Thief's Fast Hands, the Arcane Trickster's Mage Hand Legerdemain. But you could just give those subclasses (at least situational) expertise in their particular skills.
From a balance perspective, I think this comes close if you do something to address the hiding issue, and let subclasses get double proficiency in their sphere without needing a minute. But from a character design perspective, I don't like it as much as RAW, because it makes it harder to make one rogue distinct from another. In my regular home game, I play a rogue/wizard who is painfully awkward in social situations, but is really good at staying unnoticed, noticing things, figuring out situations, and knowing stuff about magic (she has expertise in Stealth, Perception, Investigation, and Arcana). That character doesn't make skill checks against particular creatures, really, so Scanning the Mark doesn't fit her -- and indeed it would be out of character for her to suddenly be really persuasive even after observing somebody for a minute; it's not about knowing what to say, exactly, but she gets flustered and trips over her words. As the designated scout, her high stealth and passive perception are big parts of her identity, so I'm not sure how Wait a Minute would work with that. By making the skill features more skill-generic (or in the case of Scanning the Mark, specifically interpersonal), you remove the capacity to tailor your particular rogue to a particular area of expertise, which is one of the fun things about playing a rogue (and in fact, one of the things that can make playing two different rogues a radically different experience).