How do you handle rejection?

A manuscript based primarily on several smaller student studies has been rejected for publication(although perhaps resubmission is possible).  This isn't TPP's first rodeo when it comes to rejection of a manuscript, but this one was rather annoying because nothing all that negative, nothing that called into question the results, or our interpretation of them, no, rather it was the old I-would-have-liked-a- similar-study-that-wasn't-done-better rejection.  Gee, when our time machine gets fixed this study will be redone along the recommended lines.  Research projects with undergrad students often have to fit within a number of constraints: the confines of a semester, the time they have available, the materials on hand, and even the speed at which plants will grow. So you do the best study that can be done given these constraints, and with different people involved, things never quite match up or come out the same.  As a result you end up wondering about what some reviewers were thinking?  What good does it do to say, oh, my, you only did this and that, and this, that, and those would have been better.  Why only 2 species? Well, that's what was on hand ready to go, and even with reasonable replicates, there were a lot of pots in the glasshouse. Ideally you would like lots of things, but it never seems to work out: a collection of seeds doesn't germinate, or something else limits your degrees of freedom.  And of course critiques based on such things are not terrible helpful because you can't change them barring time-travel. So you discuss the reasons and then fix up any real problems, you wave your arms about limitations, and resubmit.  Still it was a learning experience for the students, but a small publication would have been nice and it still may happen.