The same could be implemented using merged mining, but no matter how you look at it, merged mining is technically a more complicated solution, because it requires an entirely new blockchain one needs to reason about. You need to think about the hashrate of this separate blockchain and to encourage miners to merge-mine it, things that are just not needed when you directly encode things into the Bitcoin blockchain.
Mastercoin is different from your typical merged-mined alt-coin: it does not rely on validation by miners, it only requires timestamping.
And so you can just use Bitcoin blockchain for timestamping and enjoy security of full Bitcoin hashrate.
As far as software development goes, I'm super lazy - I do not like to do something complicated if I can do something simple that serves the same purpose.
Well, the difference is that fees will likely be order(s) of magnitude lower on the alt-chain. So there is an incentive to use it.
As for laziness, if Namecoin devs were able to implement merged-mining without any funding, and you cannot do that having $500k in the bank, why should people trust you?