This sounds like the classic Superman vs. Batman debate. I'm a Batman fan myself, and while in a head up fight there really is no competition...I also believe, given the right equipment and his own creativity Batman will beat Superman. Even though by all measurements, Superman is inherently superior to Batman.
I think he did once actually... In a fight over wonderwoman...
Lasso of truth... Man you got some big

As for Magic shops...
I've never been a fan of the idea of walk in and buy whatever you need magic shops. Just seems to unspecial. Buying magic items easily seems to make them viewed as fundamentaly no different then say a horse, or a normal weapon.
That said, I DO have magic shops, and people with magic items to sell in ym campaigns. Just not everything is available, and not all at once. I think saying that magic items are never available for sale is kind of strange and counter to human nature. If something is useful and makes life easier, then people will want it. If people want it, someone else will be looking to profit off of that want. So someone will sell it.
The blacksmith might have magic swords and armor, there might be an old crone with potions, or magic tatoos... etc. Some stuff needs to be comissioned.
I think if you're looking to make magic items really "special" in your campaign you have to do one or both of the following:
Get rid of all the common magic items, and only go with artifacts.
Give magic items some sort of drawback to their use. IE using them causes a loss of healing surges, or harms you in some other way.