Changing tick intervals when x axis values are dates

Have you tried this:

> p + opts(axis.text.x=theme_text(angle=-90))

making the ticks vertical sometimes makes all text fit and therefore appear.

Upgrade comment

You can change the x-axis labels using scale_x_date and formats from the scales package. Using the code from the ggplot2 scale_x_date help pages

library(ggplot2)
library(scales) # to access breaks/formatting functions
    
# Change Date to date format
aaci$dt <- as.Date(aaci$Date)

# Plot
# You can change the format to suit your requirements
ggplot(aaci, aes(x=dt, y=Average, colour=Species, group=Species)) +
      geom_point(size=4) +
      geom_line(size=1.3) + 
      scale_y_continuous(limits = c(0,100), breaks=seq(0,100,10)) + 
      scale_x_date(date_breaks = "months" , date_labels = "%b-%y")