When do merchants start paying the actual value of items without bonus effects and perks?

Sounds like you have low Speech

Speech will directly affect the prices paid when buying from and selling to merchants, even without the assorted perks. At 0 speech, merchants will sell items for 3 times their base price, and buy for a third of their base price. At 100 speech, merchants will sell items for twice their base price and buy for half.

The value in your inventory is the worth of the item. Vendors will give you a percentage of that value based on your speechcraft skill and other factors. Likewise they will sell it for a multiple of that value.

Specifically the price is:

Sell price = [ value of item ] / [ 3.3 - (1.3 * [speech skill]/100) ] 
           * [(1 + Haggling %) * (1 + Allure %) * (1 + Fortify Barter from potion) 
           * (1 + the sum of Fortify Barter from equipment + Fortify Barter from Blessing of Zenithar)

From the UESP Wiki.

Are you using your perks on speech at all? You need to pick the basic speech improvement perk at the bottom of the tree. It'll get the vendors to sell at a much better rate. Simply ramping up to 100 will help a bit, but not nearly as much as the perks.