It looks like it is premature to waste time "innovating", we should first just clone as many identical chains as merged mining can practically handle, get them all up to difficulty matching bitcoin's and only *then* worry about which ones to make which changes to to develop various innovations or changes.
Until we actually have a whole strign of secure chains to innovate with, speculation as to what innovations might prove good is kind of moot. First lets actually secure some chains. If we can do that, fine, we can look into varying them from each other. If we can't its a doomed route anyway.
Most of the people who were looking forward to merged mining as a proof that innovation might have some chance of having a point or usefulness are seeing so far that, sorry, merged mining is no help, any attempt to innovate is going to have to wait until some other way of solving the terrorist / religious fanatic / mad bomber attack scenarios before there is any point wasting thought on it.
People who didn't do their work in secret have been told that simply going merged had these kinds of risks. It is not everyone elses fault that you didn't talk to people or realize this for yourself.
Merged mining namecoin has worked out really well, because namecoin already had value— the economics were different.
You could achieve acceptable security in a new merged mining chain at its valuless birth in quite a few ways... off the top of my head:
* Pre-announce it and build excitement well in advance, convince people of its values, make sure it scratches their itches— and then when it switches on there will be a lot of people supporting it and it will be well decentralized. (Litecoin did a bit of this, but it could be better done than that)
— but doing this will require some real value from the start. Beating the bitcoin developers out of the gate in deploying new functionality they invented and coded probably won't cut it.
* Start with an initially high difficulty, so that the system doesn't do much (and thus can't be attacked much) until it has a reasonable amount of decentralization. (bitcoin itself did this, though it could have done more of it— while diff 1 sounds low today, computers and esp. software of _a lot_ faster, though the big MMed hash concentrations make this harder)
* Reduce decentralization initially— program it require frequent signed checkpoints (or something like SC2's alternative blocks) _until_ the system has a high enough difficulty to stand on its own (enough is easy to figure out for a merged chain, since you know how much hash power is out there), or until a certain number of blocks pass.
* Raise some BTC and pay existing miners on the merged chain to cooperate, until your chain is big enough and worthwhile enough to survive on its own merits— setting up a new merged chain has a cost, a fairly high one right now because the support is not well integrated. Your own system didn't work with a lot of popular software. You can't expect disinterested parties to just mine your coin because its easy to do so, — hell, for most pools mining it requires writing new code. So you get only the interested parties and with that comes good and bad.
The last is probably the most interesting, simply because for any decenteralized system which doesn't claim to be a deflationary (or at least effectively deflationary for early adopters in the short-medium term) currency, externally paying miners to support it is probably the only way to bootstrap.
Though, you may note that all of these tactics reduce the ability to pump and dump new clone-coins. I consider this a ecological feature, rather than a bug.
(To be clear— I don't have reason to think _you_ were trying to build a pump and dump altcoin scam, I don't know what you thought you were doing— but _other_ people in the altcoin community were super eager to participate in one, and I think the evidence is basically clear enough on that. It just turns out that they care so little about doing so, or are so greedy about it, that they won't put in the resources to undo the attack against coiledcoin)