You cannot do this with a theme. But you can save your axes preferences and then add them to your plots. Or define your favorite versions of ggplot
in a function:
require(ggplot2)
# define my favorite axes
x.axis <- scale_x_continuous('this is x', breaks=seq(0,10,by=2))
y.axis <- scale_y_continuous('this is y', breaks=seq(1990,2010,by=3))
xy.ggplot <- function(...) ggplot(...) + x.axis + y.axis
# use axes in plots
ggplot(mpg,aes(x=displ,y=year)) + geom_point()
ggplot(mpg,aes(x=displ,y=year)) + geom_point() + x.axis
xy.ggplot(mpg,aes(x=displ,y=year)) + geom_point()
# you can also overwrite ggplot
ggplot <- function(...) ggplot2:::ggplot(...) + scale_x_continuous('this is x', breaks=seq(0,10,by=2))
# use your version
ggplot(mpg,aes(x=displ,y=year)) + geom_point()
# to get standard ggplot
ggplot2::ggplot(mpg,aes(x=displ,y=year)) + geom_point()