A few thoughts:
1. 3e magic item creation rules are beyond annoying; if 4e does away with them it could easily be the best development it achieves. PCs should not be making magic items.
2. Believability goes away all too quickly if the items in a particular adventure just "happen" to be those that are best suited to the particular PCs - the voulge-guisarme example from earlier is what I mean.
3. I've always allowed characters to "commission" creation of a magic item, usually through a wizards' guild. The PC asks if item x can be made, and if it can the guild collects half payment up front and tells the PC to come back in anywhere from a few weeks (for a simple potion or scroll) to a year or more (for something complex like a +3 Frostbrand Defender sword with a once-per-day Dimension Door) to collect the item and complete payment.
4. The idea of a magic "shop" never really flew with me, but the idea of there being some amount of trade in magic items makes loads of sense. Logically, it would happen in one of two basic ways: different adventuring parties get together and barter, or some group - the local wizards' guild (or, for weapons and armour, the warriors' guild) seems the most obvious - acts as a clearing-house. It also makes sense that just because a particular party can't use a given item doesn't mean nobody can - somebody somewhere is proficient in that wacko weapon you just found, and has the money to buy it; all you have to do is find her.
4a. The only time a magic shop *does* make sense is if it is acting as a fence for the local Thieves' guild, selling the magic items that the guild members have managed to steal.
5. Magic really should be easier to break/destroy/blow up than 3e has it. 1-2e had it right, even if the rolling sometimes goes on all night to sort out the cascading destruction.

That way, the players can more often have the fun of discovering new stuff and finding out what it does...
Lanefan