We collected data on the natural regeneration of Balanites aegyptiaca by using stratified sampling design with three levels of stratification, so which model can be better for data analysis?
The linear (mixed) model is just a special case of the generalized linear (mixed) model, and the choice should depend on the nature of your data. For count data, use GLM(M) from the Poisson family, for binary data a logistic regression model, for continuous data you may use a linear model.
I'm not sure which software package you're using, but maybe this overview is helpful: