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?
If Mastercoin fees become a problem, we could always migrate away to a separate blockchain (and it's not 100% that they will be).
Right now this is the fastest route to push development forward.
We'd rather spend the $500k to implement features, not infrastructure that may-or-may-not be needed.
Still, when the time is right, various optimization features will warrant bounties of them own.
If a separate blockchain is deemed necessary because the Bitcoin blockchain is drowning in Mastercoin transactions, and this is really the way to keep Mastercoin fees at decent levels, then I'm sure a part of the 1Exodus funds could be allocated to investigating this option.
However, this burdening is something that Bitcoin users and developers will just have to live with. Nobody is the boss of Bitcoin, and any standard Bitcoin transaction (like Mastercoin transactions are) are legitimate transactions that Bitcoin simply has to learn to deal with. There is just no feasible way that I see that Bitcoin developers could ban such transactions (please enlighten me if I'm wrong).
If the devs were able to do this -
http://bitcoinmagazine.com/4465/bitcoin-developers-adding-0-007-minimum-transaction-output-size/ - they can ban Mastercoin transactions. Bitcoin's decentralization is just a myth. All big pool owners will do what Gavin and Co. will ask them to do.
I hardly see Gavin or the core devs, or pool operators for that matter, trying to outright ban or slow down Mastercoin transactions, which are always above the dust level and pay all required miner fees.
Mastercoin can adapat if needed, but I don't think it will come to that. Gavin and the core devs will not want to play a game of cat-and-mouse with the Mastercoin protocol - they have far more important things to do. And I'll add that Mastercoin developers aren't just ignoring everything Bitcoin devs are saying - rather they are rather cooperative in finding better, more optimal ways to encode Mastercoin transactions. It is possible that a sort of merged-mined alt-chain will be deemed the optimal solution one far day in the future ... but for now it's certainly not the case.
The entire merged mined / timestamping service approach to Mastercoin should just be viewed as a possible future optimization, and as we know optimizations are best implemented at the correct time, and not before.