#1) Part of the "rub" here is this: after about 10th level, the Rogue's Hide skill is useless, in part because of all of the creatures that "automatically" detect him. Case in Point: Blindsight.
I think this depends in part on how one adjudicates blindsight and how the character is hiding.
How does Blindsight work, in other words?
Also: asking the players to be "creative" when hiding begs the question: "What are ranks in hiding good for, if not for knowing of ways to hide?" Or "Why should I, a 21st century couch potato, know more about hiding than my 18th level rogue?"
Because Disguise Scent (or whatever) isn't a skill yet; it's presented as a challenge to players. You're saying you'd rather deal with it through a skill check. This is no more or less reasonable than having, say, Diplomacy as a skill check.
It's reasonable to say that a PC that deals with Blindsight and Scent all the rest would naturally develop ways to counter them as part of his natural skill set.
It's also reasonable to say that players either should or may deal with these challenges directly.
From this angle, it's a question of style.
Why is it that a creature can't automatically see something, but can automatically smell, blindsight, tremorsense it....even if the smell (for example) is faint or hidden? Why not have a skill roll for that?
Well; creatures
can automatically see and hear things. The point is that there is no skill that currently counters scent etc.; that's why they're automatic. No one tries to 'hide' from them.
I imagine that the reason for not presenting Scent as a (counterable) skill is because it is so different than seeing and hearing. None of the core PC races has a scent ability; it's simply not in the typical experience of a PC (or player), as things now stand.
Simply adding it in to an Awareness skill that takes seeing and hearing as its base will prove problematic, at least to the extent that it will require a number of situational modifiers (wind, medium, potency, etc.) to provide even a minimal degree of verisimilitude (rather than simply balance with player expectations for high-level PCs).
As to differences in ability, ranges deal with this issue to some extent.
Adendum: I want new rules to be simple, possibly even simpler than what I started with. Having a separate "see" and "hear" and "smell" and "tremorsense" skills is not simpler (and requires more skill points!), and it's not a better system than what we have presently.
That makes sense, but any reduction in complexity on the skill side will require some increase in complexity on the situational side. You'll have to begin to keep wind direction in mind and so on. This is really no different than keeping track of, say, illumination, but is in addition to it.