Keep in mind that whenever an alternative chain enables merged mining it is centralizing a huge amount of trust in the bitcoin ("Nakamoto chain") mining pool operators.
When people join a bitcoin mining pool, it's generally because they want bitcoins. Sure, a few people will ask their pool operator to add thischain or thatchain mining, and some pools will. But plenty of pools won't.
Anybody running a pool who has not told its miners "hey we are mining blartzcoin and I will split the reward with you" basically has a gigantic pile of blartzcoin hashpower to direct as he/she pleases. They're totally unaccountable in how they use that power. If they use it to screw up the alternative blockchain, and in doing so they sacrifice the altchain mining rewards, none of their miners will get upset and jump ship because they weren't expecting those rewards in the first place.
Merged mining is risky for altchains unless you can be reasonably sure that miners will demand that their pools mine that chain. Right now I think Namecoin is the only case where that's even close to being true. It's also the only chain with a coherent answer to the question "wait, doesn't bitcoin already serve this purpose?"