Its not really magic users, its magic gear.
Slippers of Spider Climbing really embody the problem. They grant a climb speed. Once that happens, it doesn't matter what your climb skill looks like, or what your armor penalty looks like. They completely negate that entire aspect of your character.
So you get in a weird situation. If you give them to the guy who likes to climb, they're redundant with his climb skill ranks. If you give them to someone who's terrible at climbing, he's significantly better than the guy who invested valuable skill ranks in climbing.
My wizard casts grease on your slippers of spider climbing. It may not get you the first round, but it will sooner or later. Looks like you're going to fall, too bad you chose not to take ranks in climb, you might have actually had a chance at the +20 DC climb check to catch yourself. Sure, spider climb gives you +8 and take 10, but without any ranks, that's not enough. And sure, maybe you have feather fall on the ready to not die. But now you're on the ground, in range of Meathead the Fighter's oversized greataxe.
Spells can make a rogue's abilities obsolete, but at least they run out, or require the spellcaster to fill up spell slots with Knock instead of an attack spell. Its gear that creates the problem- a 50 charge Wand of Knock can last most parties a very, very long time, and isn't all that expensive.
I agree spells that auto-win a skill check stink, and listed it as a problem with 3E (in the 'what's wwrong with 3E?' thread). Most 3E players won't argue that. However, this is at least in part due to carryover from 2E, and is easy to fix (houserule).
And that's not even getting into the ways that advanced magical tricks like flight and teleportation rain on the parade of classes based on mundane maneuverability.
It depends. MIC made short range teleportation items cheap enough for all to use. Flight, I've found, is sort of like having a tech advantage. At first, it's killer, later on everyone has it or can deal with it. At level 5, flight is a real game-changer. By level 10, most PCs that bother to can have flying abilities of their own from items or elsewhere, within reasonable expense. And even at level 5, a Wizard trading scorching rays with a full BAB character using a bow he has no feats for has only a slight to moderate advantage, with hp differences. And it's possible he'll run out of strong ammo before the fight's over if he has some unlucky misses.
It can do it better... fewer times per day and with more explicit limitations and countermeasures, at the expense of other opportunities.
So no. Put me in the strongly disagree column.
I put slightly disagree, but I concur with your reasoning regardless.
Very much so. Gets so bad the rogue is better off marginalizing his OWN skills with magic!
Why bother attacking AC? UMD a wand of a [range] touch attack spell!
Undead? Break out the sorta cheap Staff of fire and Use the No save, double damage to undead Wall of Fire.
Mid level? Buddy up to the wizard for Blink or Improved Invisibility!
High level? Buddy up to the Druid for some 12d6 to 20D6 + Sneak fire seeds!
You call it marginalizing. I call it supplementing. Rogues are crafty, they don't cry about the abundance and power of magic, they put it to their own use to help make their jobs easier.
UMDing a wand with a touch spell is just plain brilliant against foes with massive natural armor.
Using items to face undead is nice too, but why even go for damage dealing? That gets expensive. Get some nice battlefield control for those occasions -- scrolls of web, entangle, etc...
As for wizard buffing, why not? Two characters combining their abilities for a result greater than the sum of the parts put in? That's




ing beautiful, man.

Fire seeds is nice, but still fire damage. Why not get a wand of acid splash for 375 gp and not even need another character? Sure, you lose the 12-20d6 base, but for that low cost and your skill in sneaking, you now have 50 uses of d3 +xd6 acid damage that ignores SR. One man's crime against nature is another's ingenuity, I guess.
You are again discounting scrolls, wands and other easily craftable items.
As for explicit limitations and countermeasures - realy? your saying, under 3.5 rules, it's easier to countermeasure a wizard determined to get at or find out something than a rogue?
Rogues can use all those items, as well. I really consider UMd a class feature, more than a class skill. It gets the rogue through encounters against SA-immune foes, and greatly expands his options.
As for counter measures... pretty much the entire schools of abjuration and divination exist to foil the other schools. I really don't feel like listing every single instance, but take disguise, for example. There are spells to give large bonuses, yes. But there are also many spells to see through them, not to mention the possibility of a spellcraft check to know a disguise/alter spell was used (which will result in
bad stuff even if the disguise itself isn't seen through). However, there is NO way to pierce mundane disguise methods, such as a kit or huge ranks, other than actually winning the spot check. As long as the rogue can keep his important skill mods high, there's not much most enemies can do to stop him, aside from also keeping their modifiers high.
So, I put sort of disagree because while I think Rogues have the skill list and guile to most put magic to use, I do agree the existence of some things (knock, etc...) do nothing but let some old guy from an ivory tower suddenly become the greatest lock picker on the street, for example. Even so, 3E offers a Rogue character the most fun and variety of any edition 2E-4E in my experience (and those are the only ones I've played). Which is the most important thing.