proto and baseenv()
In end it seems that your real beef is with R so perhaps you should be using a different language.
In my case you may be right. I do think there are a million things wrong with R. For instance, I was looking for a package that overcomes two of the problems R IMHO has: namespace pollution and the lack of an easy-to-use standard object system. Should I be using R? I do keep asking myself that same question...
With respect to proto its really just discussing whether to use proto(baseenv(), ...) vs proto(...)
Unfortunately this doesn't fix the problem as was noted earlier:
z <- 1
proto(baseenv(), expr={a <- z})$a
Error in eval(expr, envir, enclos) : object "z" not found
Also, your alternative likely would be unusable due to performance whereas proto is fast enough to be usable (see list of applications that use it at http://r-proto.googlecode.com/#Applications). Its not as fast as S3 (though sometimes you can get it that fast by optimizing your code). The development version of proto is even faster than the current version of proto due to the addition of lazy evaluation.
This make sense to me.
Ben Escoto