You are always welcome to fudge it, or not use the weirdo magic item economy in Pathfinder, but if you are wanting to go by the rules, you are doing it right. Higher DCs are supposed to cost that much more. Just like a +1 sword to +2 to +3 grows in cost squared, DC increase isn't priced linearly. A DC 14 is a lot less useful than a DC 17 and so the cost being 3x as much is how the system works.
You can try to eke out more "according to the rules" by adding cheesy limitations to the item to drop the cost, but it would be best to just wing it the way you want it. Unless you're publishing it, no one will care except inasmuch as it advances the play of your campaign.
I think there's two reasons why it would make sense for magic item creation costs to be as high or higher than purchase cost, that fit with the idea of D&D and the stories portrayed:
Most of the permanent stuff for sale is ancient
For most of it, it doesn't matter how much gp a caster once spent for it. The magic item for sale in the Bazaar of the Bizarre isn't made by the owner, or anyone he knows. It's made by an ancient wizard, who died centuries ago, and isn't going to see a penny of that money. It was probably looted by adventurers, who then decided they didn't need it all that much, so they sold it for whatever they could get for it and now it's for sale for whatever the item's owner thinks he can get for it.
The reason he asks you for 2000gp, even though you can make it for 2000gp is because A) most of the people who can afford a magic item, could also make one themselves and B) he's now undercutting any bored Wizard who tries to compete with freshly made magic gear. Considering these magic items are practically indestructible and require next to no maintenance, there's eons of time that they've been made in and most are simply still around to be found.
The market for permanent magic items is terrible because the stuff literally lasts forever and there's a whole class of people whose only job is to venture into the wilds, "liberate" the items and then sell them cheap so they can get some more potions for their next "adventure". Sellers are simply responding to this dynamic.
Most of the consumable stuff is made by specialists
The reason your Wizard takes 4 days to write a scroll and spends a 100gp on it is, for a major part, because your Wizard is a firebreathing, lightning throwing, people charming, monster summoning murder-machine and not a scribe.
Probably if you decided to spend 90% of your time learning how to write a Scroll of Burning Hands faster and cheaper than usual, you could also learn to do it in half the time and for half the cost and earn some money selling those scrolls to the other Wizards who don't perfect the art of calligraphy but instead waste their time going out to kill things and take their stuff.
You simply cannot reasonably compete with the people who dedicate their lives to creating consumable magic items and never learn to survive adventures. (And the reason there aren't any rules for doing so is because this is Dungeons & Dragons and any such character would be an NPC, not a player character)
Why you can't make money selling magic items
Ultimately, what it comes down to is this: making a lot of money off of creating and selling magic is boring and not what D&D is about, so the standard rules don't allow for it. The above is just flavoring for why it's like this.
Any experienced DM who can turn "making and selling +1 swords" into a fun play session will have enough experience to tweak (or disregard) the rules so that it works.
Any DM who doesn´t have that level of experience cannot accidentally screw up his game by showing his players how to make loads of money without actually risking their hides in the adventures that the game is about.
It's a win for everyone.
Best Answer
Wish had specific rules for magic item creation only in 3.0/3.5e
So far as I can tell the only editions in which the use of wish to create magical items is well-defined are 3.0e and 3.5e.
1e/2e AD&D
1e/2e AD&D rules contain the wish and limited wish spells, but don't describe how these spells could be used to create magical items. Limited wish explicitly cannot do so, as described in the 1e PHB:
The best a limited wish can do here is give you information that might help you acquire a certain magical item, but it certainly can't create one for you; and the DM is encouraged to ensure that "greedy" desires end in disaster regardless.
The full-fat unlimited wish doesn't have the same restrictions, but it also doesn't describe how it might create magical items. The best we can determine is that such an application would come under the "other forms of wishes" described by the spell (as it's neither healing, resurrection, or transportation) and so the caster would be subject to some exhaustion from the casting. Ultimately these rules leave game balance in the hands of the DM/referee and so it's up to them how to interpret a wish used to create or acquire a magical item.
The 2e versions of these spells have largely the same text and work in the same way.
3.0e
As with the editions before it 3e has limited wish and wish spells available to cast. Limited wish still can't create magical items - its use is restricted to replicating other spell effects of up to 6th level, undoing certain other harmful spells, or freeform effects "whose power level is in line with" those other uses, which definitely doesn't include creating permanent magical items. The unlimited wish, however, absolutely can create magical items, as one of its uses is:
As the spell text notes, wish can be used to attempt greater feats than those described, though at risk of perverting the intent of the wish or achieving only partial fulfilment; this text introduces the example of wishing for a staff of the magi that was subsequently re-used in 5e:
At any rate it's considered safe to use a wish to create a magical item so long as that item is worth no more than 15,000gp. The cost of casting is measured in XP; casting wish for any purpose drains 5,000XP from the caster. This edition frequently used XP as a cost for certain very powerful spells, and in the normal magical item creation process, where a creator would normally have to pay 1XP per 25gp of the item's base price - 5,000XP would thus equate to 125,000gp worth of magical item if crafted the normal way, so you pay a very expensive premium if you instead use that XP to cast wish (but you do get the item instantly, and without the mundane material costs.)
3.5e
The 3.5 revision made some changes to how wish works, especially with respect to using it create items. In contrast to the 3e version, a 3.5e wish can:
This introduces the specific ability to create arbitrary nonmagical items of up to 25kgp value, which was retained in 5e's wish, but also has the ability to create magical items, and it does so seemingly without restriction. A nonmagical item can't cost more than 25kgp, but no price cap is given for a magical item! However, there is actually a limit to what can be created using this wish - it's implemented as an XP cost:
Thus the limitation on this use of wish is how much XP the caster has available to spend upon it. 3.5e has the same XP costs for creating magic items as 3e did, so for example to create a magical item worth 25kgp would cost 7,000XP (5,000XP for the base cost of wish plus 2,000XP to cover what would normally have been a 1,000XP cost for the item).
This mechanic puts a hard limit on how valuable an item a caster of any given level could afford to produce, since the maximum free XP they could possibly have to cast on spells is 1 XP less than their current level times 1000 - if they had any more XP than that they would have levelled up, and they can't spend any more XP than that since the rules don't allow spending so much XP that you would lose a level. A 17th level wizard who was just 1XP away from levelling up to 18th would have 16,999XP and could thus create an item worth at most 149,975gp, presuming they were were willing to sacrifice all their progress to the next level. (This mechanic does interact badly with certain creatures who have access to wish as a spell-like ability rather than as a spell and therefore ignore its XP costs, as they could then conceivably create any arbitrarily valuable magical item.)
For both 3.0 and 3.5e there is another possible application for limited wish and wish spells in the domain of magic item crafting; the normal crafting rules usually require an item's creator to have the ability to cast a certain spell or spells as appropriate to the item's nature, though have exceptions for the ability to provide the same spell effect through some other means such as a cooperating friend or another magic item that already duplicates the spell. Since the wish spells can be used to duplicate other spell effects, it seems reasonable to extrapolate that they can be used to meet the spell-based prerequisites of crafting magical items normally (as in this question).
4e
In 4th edition there is no wish spell available, so there's no possibility to use one to create magical items.