Form has a great influence on players value. Also, his skills, obviously, but the skills change happen once every couple of weeks, while form can go up and down (max 3 levels) twice a week.
sometimes a player will have a higher value than another player, but have a lower wage
again, form. maybe the first player was in divine form, thus higher value, but lower skills, while the second was may have better skills, but he's in low form.
Also, the wage changes only at the beginning of the season, maybe a player is very talented and he pops fast in multiple skills (increasing his value), while other player with same wage is not that talented and he doesn't develop well, keeping a lower value.