That brings its own problems. The math of D&D is such that the usefulness of many feats and builds depends upon equipment.
For instance, compare a 20th level fighter with fullplate and a shield (nonmagical) to a 20th level fighter with no armor and a greatsword. Against most foes at that level, there is no significant difference between AC 20 and AC 10. Every attack will hit except on a one either way. Let's pretend for the moment that the sword and shield fighter has a 13 dex for dodge with a 16 strength and the two handed fighter has an 18 strength to take full advantage of his 1.5 str bonus. Going from AC 20 to 22 makes no difference for the defensively oriented fighter. He's still going to be hit on a one even when many foes are power attacking for ten points. Going from doing 2d6+4 (16 str assumed default) to 2d6+6 (18 str), however, is significant for the other fighter.
Now, however, take a different comparison. +5 fullplate, +5 shield, +5 amulet of natural armor, +5 ring of protection, and boots of speed. Now the sword and shield fighter can easily have an AC of 43 (with dodge) but the other character is stuck with AC 36. At that level, this is a very significant difference that will often result in the sword and shield fighter taking 2/3-1/2 the damage that the two handed fighter takes.
Because attack bonusses automatically increase with level progression but defense remains largely static, the utility of any build focussed on defense will be understated (in many cases, vastly) by a comparison that excludes magic items. Conversely, offensively oriented warrior builds--particularly barbarians--will unduly benefit from the exclusion of magic items.
And, as to equipment becoming more important than class abilities--that's always been the case in D&D and if you think it's bad now, try remembering second edition. In 3.x, there's a vast difference between a finesse fighter who started with a 13 strength, took weapon finesse, dodge, mobility, spring attack, combat expertise, improved disarm, and later duelist levels, and a bruiser who started with an 18 strength and took power attack, cleave, great cleave, improved sunder, and later took Fist of Hextor levels. Playing Baldur's Gate II, I've noticed that there's really minimal difference between how my paladin plays in combat and how Sarevok plays and how Mazzy or Minsc play--and that difference is primarily in whether he's wielding a holy avenger (the paladin), the Ravager halberd (Sarevok), or dual wielding the Sword of Mask (or Foebane) and Kundane (Mazzy) and which girdle of giant strength and suit of armor they're wearing. Feats, skills, and feat chains make a huge difference in 3.x. However, a large degree of equipment focus at high levels is inevitable. Equipment is--as described above--a large part of what makes the choices between various focusses meaningful. (Also, unless you make it useless, it will add capability to characters and then the character's capability will HAVE to be measured with that in consideration).
Crothian said:
Then it becomes more important what equipment you have and not what class you are. I comparison of classes should use no magical equipment because of that.