While developing some new simulation code with S4 system I stumbled upon some big difficulties in terms of computational efficiency. That lead me to diging into archives of Rhelp and Rdevel looking for clues. I found some interesting threads that address almost exactly the same problems that I do. Read for yourself here and here, 
Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).
