Okay, so I can't get a working binary on my Mac right now, but I can delve through the source code, and that has been very enlightening, namely, that Namecoins really are just colored coins! I had thought that the Namecoin alt had modified the transaction structure in some way to handle setting the value of the registered name, but that doesn't look to be the case. Instead, Namecoin uses the Script of the transaction to set a value, and enforces that subsequent "name_update" transactions absorb the most recent unspent transaction of the same 0.01 NMC that was used to initialize the name in the first place. Namecoin usurps a few of the Script constants (namely OP_1, OP_2, and OP_3) and gives them special meaning. It constructs the Scripts to properly validate with the standard Bitcoin parser (it uses OP_DROP to drop off its special values before continuing with a standard transaction Script).

Namecoin's blockchain is at the same speed as Bitcoin's (10 minutes), and uses the same hashing methodology, just the genesis block is based on a different string. That aside, it looks to me that Namecoin's transactions would qualify as valid, non-standard Bitcoin transactions (non-standard because they use different opcodes in their Scripts). As far as I can tell, most all the other changes to the Namecoin source compared to Bitcoin's are to implement the merged mining idea.

So... given that "non-standard transactions" might be entering the community's awareness more, due to 0.8.2 marking microtransactions as non-standard, the question that comes to my mind is why is this an alt-chain at all? The same mining pools that have been convinced to run namecoin pools, could probably be convinced to run pools that accept non-standard Bitcoin transactions (or specific non-standard transactions that conform to a "namecoin standard script") instead, and "namecoins" could become colored Bitcoins with a particular script giving them a data value as well. Is there a strong benefit to having this be a completely separate blockchain?