1.2 PRIMER has some down sides
Like any software package, PRIMER has some down sides.
PRIMER has a pretty specific niche
As already mentioned, PRIMER's focus is on non-parametric and semi-parametric techniques and graphics for analysing multivariate data, particularly ecological data. It doesn't offer much in terms of standard classical statistical methods, graphics and modeling. In truth, there are a host of other software packages out there that already do that sort of thing (SAS, JMP, SPSS, Stata, Matlab, R, etc.), and PRIMER has never aimed to compete with any of those.
This means that PRIMER (typically) cannot (currently) serve as your only software tool for data analysis. It is admittedly rather a pain to have to (potentially) swap between different software tools to accomplish all of your desired stats for a given project. The PRIMER-e team is always seeking to develop PRIMER for the future, not only within its niche, but also to progressively embrace an array of existing statistical methods (classical or otherwise) that are useful, particularly for ecology. (Note: If you have ideas about this that you'd like to share, particular things you really wish were in PRIMER, then please contact the team at PRIMER-e directly: primer@primer-e.com.)
PRIMER is not free
The PRIMER-e team is small and consists of very dedicated individuals. We have to support ourselves and our families, so the PRIMER (and PERMANOVA+) software is not free.
PRIMER is not platform-independent
PRIMER runs on a Windows operating system. It cannot (yet) be run natively on Linux or Mac OSX, but it can be run via virtualization software.
PRIMER doesn't (currently) have scripting
When you use PRIMER, you do not have to mess with any code. The clear down side to this is that there is no way to modify PRIMER to do extra things (or different things or multiple things) beyond what it currently does, but that you might really wish it would do for you.
This also means that you cannot (currently) create a 'script' inside PRIMER. Perhaps you want to run a particular PERMANOVA design a thousand times (e.g., on simulated datasets), or maybe you want to implement the same series of steps in a bespoke analysis pathway routinely (e.g., every year when your monitoring data comes in) or on multiple datasets. It would be really nice to have some sort of scripting tool within PRIMER that would allow things like this. (Watch this space!)