I agree on the base prices for items since they don't really fluctuate much except for MS. It's kind of already the case btw, I don't see much changes on the item prices to be honest.
But for pokes there are way too many variables : rarity, IV's, evo stages, EV's trained/not, nature, ability etc.. A lot of people would tend to set stupid prices whenever they have a poke with 31 IV in atk and an Adamant nature, just because 31 and Adamant...Same as buying a Gale Wings Talonflame for million only for its ability when you can farm it at TV or wait a for a stage 1 sale. I mean yes it's stupid but it would be even more stupid to buy these. So it's all on you to determine if a price is right according to all the poke's specifications. It doesn't ask much to just do a little research on every poke you want, have the patience and say "wait this is too expensive I'll wait for another one".
What I was thinking was like a pokemon deposit/trading system in which you just put the pokes you want to sell (just like GTS on consoles), you set the minimum price you want for each and every poke you sell, like instant prices would be a category in this system. Or you put your pokes in the auction category, maybe set a minimum starting price and just wait for people to bid on them. But I guess it would be such a big task for coders. And personaly I'd prefer the admins focusing more on the game itself rather than the trading system xD
It's just up to us not to buy anything at any price after all..