I agree merged mining can be beneficial, possibly even critical, to complementary block chains. As you point out it's a win-win by sharing resources to different tasks.
Peter Todd gave an interesting perspective on a LTB episode which is merged mining can encourage mining centralization. This is due to conflicting incentive vs resource requirements to merged mine. Independent miners need to maintain updated block chains for every coin mined which can offset monetary gains, whereas pools can manage the overhead while still offering the gains. The more chains providing incentive to merged mine, the greater the incentive to join a pool, especially one offering the most chains, undermining things like P2Pool.
I'm thinking (and hoping) we'll see many more pools spring up to counter the recurring theme of a single pool or a few comprising worrying percentages of global hashrate. However, I think it's also healthy to have a large number of independent miners. A healthy mix of pools, enterprise miners, hobbyists and independents I think is probably best. Just something to consider.