It has nothing to do with sha-256 or scrypt.
The issue is not if it is technically viable, of course it is. The issue is either getting coin developers to agree and work with each other to set up merged mining, or fork one or two chains separate from the official coin development and hope you get enough miners on board to keep both forks alive.
Remember one chain has to accept the others chains POW as a valid POW on that chain and become the "aux" chain, and well you can kind of see where pride might get in the way.
This is not to say I am against the idea, personally I think it might be helpful in strengthening the strongest of the new alt-coins. However, it is a long, tough hill to climb. With the alt-coin community split like it is today, I have a hard time seeing it happen.
So what's to stop an alt-coin dev from creating a coin and then creating a second coin that you can merge mine with that first coin? That wouldn't be hurting themselves and would give people incentive to mine their coins because they could get multiples of different coins with the same hashes. Also, how far could this go? Can you only merge mine one coin on top of the original coin, or could you simultaneously merge mine multiple coins on one main coin, or have a chain of coins merge mining themselves?