Why the Secret Spell Scroll system would have never worked.

But it doesn't CREATE any mesos. The problem is the excessive amounts of mesos flooding the economy. There is too much mesos, and mts is not where it came from. mts assists the process and provides motivation, sure, although it isn't the root of the problem. Once the duping stops, mts will stop being a problem. Even without mts, duping would still be a problem. Unless they stop the duping, MS is totally screwed quite frankly.

Also, from my understanding the SSS actually evade trade tax.

I think getting rid of the MTS would be ideal in cutting down a great amount of duping, because it provides so much incentive. Easy access to large amounts of NX makes it that dupers incur no loss when attempting to dupe (Like in this case each dupe required a Mushroom permit) and also profits from the MTS are much easily sold in the real world as opposed to mesos.

The other huge problem with the MTS, is every time Nexon does a rollback, the MTS/NX is never affected, so any ill gained NX remains, and any NX spent is refunded...

If a Cashshop trading room is implemented instead, it would be less advantageous to Exploiters and much more advantageous to actual players.

If the only fear of a CS trading room is that Dupers can dupe Cash shop items en mass as well, then they should make all CS items untradeable after an initial purchase from a user. This again will make it so Exploiters have to initially invest large amounts of their own real money to attempt duping. The added bonus is if Nexon is losing profits from duped CS items, they are more likely to react IMO.