Is a single longitudinal model better than two independent analyses? I'm planning to study a variable from a group of patients before and after a particular operation. I do not want to, or plan to, compare measurements across the "before" and "after" data (that is, I wasn't planning on using methods for serial data - i.e. mixed effects. GLM). I only want to compare data at the preoperative time point and then also compare data at the postoperative time point.
I was planning on using one-way ANOVA for the preoperative data and then a separate one-way ANOVA for the postoperative data (and potentially using nonparametric methods if data was not normally distributed). However, a colleague of mine is suggesting that I use longitudinal methods instead (even though I don't want to compare across time) to compare all the data. 
It never occurred to me to do that since I'm not interested in the "before" and "after" comparisons, but is that okay?
Does putting that all into one model give me an advantage compared to doing do separate ANOVA? If so, how does that change the power?
 A: You probably won't be led to a false conclusion by doing two anova's, especially if your sample size is large. But I can't give it two thumbs up (maybe one thumb).
The difficulty here is that your sample size is the number of patients. If you analyse the pre time separately from the post time, and report p-values for each, you are analysing the data as if you had done two independent studies with a total of $2n$ patients, when you actually have $n$ patients seen twice. So let's say that Mr Smith from group 1 is an outlier with weird hormones. Then Mr Smith's weird hormones will show up again post-op, only your proposed analysis does not take that possibility into account. It assumes that Mr Smith post-op is "not the man he was".
Data should be analysed in a way that reflects the randomization and the study design (I'm a frequentist). That said, the practical consequences will probably not be large. But you are setting yourself up for negative comments from whatever snarky methodologist reviews your paper if you treat the data as if they came from two different studies when it actually was longitudinal. And if your study is small, like 3 patients in each group, you really need to go longitudinal.
