Stratum is not limited in terms of merged mining. It's a matter of adding merged mining to the pool software. Both Slush and BTC Guild have elected to stop supporting NMC with Stratum due to complete lack of development. NMC is based on bitcoin 0.3 code, has had NO active development in over a year. It is a failed experiment only being kept alive by people taking advantage of others with pump & dumps.
I know... As you have my backup pool I need to use getwork because of that. And so what. As long as it has value I don't even care why... Unless you are saying this is not for making money but experiment in bettering humanely... If this is the case you can give me all extra BTC that you don't need for running the pool.
Use a pool that supports merged mining or start your own pool, instead of spending that time whining like a child who has not got their own way maybe?