I agree with all of your points, yet I still find myself using R on a day to day basis instead of python. My reason for doing so is the large number of statistical packages that exist for R. I know that scipy exists, but it does not seem to have nearly the same coverage as CRAN + base libraries... Are there other python libraries I should look at?
it's true that CRAN+Bioconductor have a lot of coverage of statistics. if you need to fit a particular kind of model and it's not using MCMC then perhaps it's the best you can do if someone has already written the code.
we use sage (http://www.sagemath.org/) which includes a lot of the common python numerics: numpy, scipy, matplotlib, networkx. it provides nice interfaces to R and gp/pari.
i also use mayavi2 for 3d plots (something i could never get R to do well under linux...) enthought have a lot of nice things for python and scientific computing. there's also pymc which i've not used (i just write the MCMC code directly).
