1) the limited number of uses for spells as opposed to unlimited skill usage.
The real limitation is the number of meaningful opportunities to use spells/skills. Saying a thief can pick a lock an unlimited number of time per day is meaningless unless the party encounters an unlimited number of doors during the adventure.
2) the tight definition of spells compared to skills, which really have broader, more open definitions
My experience is the exact opposite: it was far more common to see spells used in creative/non-standard ways.
3) magic has limitations in a properly designed setting that intelligently considers the implications of the D&D rules that creates opportunities for skill users.
Trying to the keep all of that in balance is frankly, a pain in the ass. The Magical Arms Race of measures and countermeasures (even
reading about play like that in SepulchraveII's terrific Wyre Story Hours was too much for me). To use a comic book analogy; it's constantly trying to find something for Green Arrow to do when Green Lantern and Martian Manhunter are also in the scene. I prefer a system that makes my job as DM easier, not harder.
I've run multiple campaigns above mid level, one to the 22nd, and the rogue and the monk had plenty to do with their skills.
You're a better man than I, Gunga DM.
I think it's faulty thinking to consider only a limited set of skills when entertaining solutions to a problem.
Recognizing that there are a core set of heavily used skills isn't faulty thinking.
Further, it's inflexible on the GMs part to not consider the tasks which a character would be good out when designing adventures.
Agreed, but that isn't what we're talking about. We discussing whether the magic system should render the skill system obsolete, and if it does. Which it does.
If a character is good at carpentry, someone would seek them out for a task related to that skill.
I'm sure this comes up a lot in Jesus Christ Superstar d20 (and I would
so play a campaign of that). And again, we're not debating whether carpentry has a place in the game, we're debating if it's made useless by the existence of the Fabricate spell.
Finally, the player should be proactive in thinking of ways that they can leverage their unique skills in creative ways to help the group achieve success.
Sure. That's how my group plays. But it doesn't change the fact the spells eclipse skills in 3.5. They are simply more powerful assets, even in 'creative' play, and there limitations are both too easy to circumvent as a player and too difficult to enforce as a DM.