The choice of organism is critical. One view is that we should experiment with the simplest possible organism, perhaps Mycoplasma capricolum, which has the advantage of a small genome, and is already sequenced. But, it is difficult to culture, and few workers have experience with it.
Another view espouses the standard biological prokaryote, Eschericia coli. It, too is now sequenced, although with a genome twelve times as large. Extensive experience and the wide availability of tools argue strongly for its adoption.
A third view proposes that we use a eukaryote, specifically the yeast, S. cervisiae, as an ideal organism, because of its richer genetics, isolated nucleus, and more complex transcription mechanisms.
Our current approach favors the use of E. coli due to its wide availability and overwhelming popularity. Eventually, the advantages of using a dramatically simplified cell seem large. Engineering such a simplified cell may be an important early goal.