The system works, as it is. If you want magic without items, here's how...
"Disposable" magic items (potions, scrolls, etc.) work as they do now. If a PC wants a magic weapon, they pay 1,000 GP and gain the ability (through whatever method the GM chooses to utilize) to make any one weapon they hold +1... Now they can have their +1 axe, staff, bow, or all three, one at a time. They want the +1 Adamantine Dwarven Waraxe? No problem! They buy a MW Adamantine Dwarven Waraxe, and when they hold it, it becomes +1!
Now the Ranger with TWF wants another magic weapon? He needs to spend another 1,000 GP, and he can dual-wield +1s. As PCs rise in levels, they can improve their "magic items", just as usual. The Ranger can use his bow as +1, then switch to dual-wielding, be disarmed, and attack with dual +1 fists/kicks. Later, he can spend another 2,000 GP to make one of his weapons +2, and later improve the other one, as well.
As for "slots", you can already combine multiple items in the same slot by paying full price for one, and half price for the additions... so no problem, there. PCs can add to their powers as they see fit, within their wealth guidelines.
This system works as well as the item creation and wealth guidelines in the RAW do. Whether that's a good thing, or not, is a decision that you'll have to make for yourself...
The benefits of this system are that a character's "magic items" become abilities that they have, not so dependent upon their items. A warrior going into battle will still want a weapon, but his bonuses won't depend upon them (just his damage!) (N)PCs' abilities can't be taken away from them (unless they're standard items), and "killing things and taking their stuff" becomes much less important. Also, NPCs can have abilities without magic items, which the PCs can't then take from them, after their defeat.
One downside is that PCs' abilities can't be taken from them, either. Someone who spends the 57,000-or-so GP to become immune to level draining is going to be just that... unless an NPC can Dispel Magic to remove it...
Anyway, as I said, this system works as well as the current rules do, IMO. You can try it and see what you think, for yourselves...