R versus Matlab in <put your domain here> has been a long discussion. I end up using both, but I find that I use Matlab for more simple things and R for things where I want the highest quality in figure output or where the extra mile of not having a fine polished IDE is compensated in the end by the results.
I agree that the argument of R having a stranger IDE is annoying, but developing one might require some extra time… but as in Open source I think that you must iterate, and often, and R as become very good, stable and powerful. Many are flocking to R even without ever starting with Matlab. That’s good.