If you ask me, there are quite a few reasons shops have become useless. For instance:
1) The game isn't as hard. When you constantly have full health, and aren't dying as often, you never find the need to stock up on potions or assisting weapons like arrows and bombs.
2) Your magic meter isn't there. At least it wasn't there in TP and PH. Not having an extra meter to replenish means there's one less thing to worry about while you're in the shops.
3) Puzzles require you use more of your head, and less of your supplies. Remember in the old days when puzzles required you to find a large quiver or bomb bag just so you'd have enough utilities to squeeze by? Occasionally you'd run out of ways to obtain these necessary weapons and you'd have to run out to the nearest store before you progressed in your dungeon. Now a days puzzles only require you to shoot a handful of arrows or a pocket full of bombs, and inbetween each use they replenish you substantially.
4) Somebody keeps replenishing the pots and skulls... I'm currently playing through TP and ALttP simultaneously, and I must say the pot and skull situation has gotten weirder. I was ok back in the day when I first realized somebody kept putting the pots and skulls back into the rooms I had just ransacked and left. Feng Shui and interior decoration is very important to some people.
But it seems that that whoever is doing this job now hasn't realized that I'm stealing the things they put in their pots and skulls. I guess they just think they're misplacing these things by accident and putting them back before mom gets home and notices. If we want to spend more time in the shops, then we have to lose the bottomless free mid-dungeon vending machines.
5) These newfangled gizmos and gadgets are all self-sustaining. What I'm saying is that we need more weapons that require ammunition to use. Everything they make now has infinite uses, and that's putting stores out of business! This is also applicable to my "magic meter" portion. Let's say the Spinner needed magic to attack, and the Dominion Rod needed magic for every use, and the Iron Boots used magic to become magnetized. That would certainly make you feel the need to keep a few extra green potions in your bottles.
6) Give the items more mileage! Temples only require, like, two items and your sword for the whole time you're there. Maybe if you needed to use a few more arrows and bombs along the way to open doors and solve puzzles you'd spend more time in the shops before hand. Why did they even include the Slingshot in this game? You use it for 3 minutes after you first buy it, and then never use it again.
7) The enemy AI can be killed by your sword in every situation. Sure items make battles easier, but remember back in the day when you couldn't kill every enemy with your sword? I'm not saying make the sword useless, I'm just saying that maybe you should run into a few baddies that can't be killed the old fashioned way and require a bit of thought instead of mindless sword slashing to subdue.
On this note, I would just like to say how perfect the oil lantern is for this subject. It's got its own source of fuel, and you can't find a bottle for it every 5 steps you take so you've got to get to a shop every now and then to refuel it. The only problem is that dungeons don't have that many dark rooms, so you only really need it at the beginning of the game, in the desert temple, and at a few other small moments during the game. But boy, if the Zelda team makes more of the items like the lantern, then shops will have no trouble down the road.
Also, if they implemented useful items that broke on occasion, or made a blacksmith shop to forge your sword, making it stronger but can ultimately wear down back to its original state, then that would also give you incentive to visit stores on occasion.