The problem with the Pandaren isn't that they look the same for both factions, its that they were designed to start neutral. Their two factions don't have a strong enough identity to make for future faction based content within the Alliance or Horde. Thus they have little to no writing value going forward. That's why Blizzard has issues with them.
Blood Elves and High Elves don't have that problem. Their stories are intimately tied to the factions they are in. Their stories almost write themselves.