A very common primer design use case is that you need primers with the exact end points of your selected sequence. I would propose a simple tick box to  select this case similar to how it is done in webprimer:

http://www.candidagenome.org/cgi-bin/compute/web-primer

The Primer3 method of giving starting coordinate and sequence length is not obvious and the interface is confusing where many students end up designing internal primers.

Indeed I mean a simple check box that forces the program to only design primers including the exact end points of the selected sequence, like in the simple webprimer interface I linked to in the previous post.

The way it is done now according to primer3 instructions is under the option "Targets"

http://bioinfo.ut.ee/primer3-0.4.0/primer3/primer3_www_help.html

I'm not sure if Primer3 add-on calculates primer hairpins. I know it calculates primer dimers. If it doesn't, here is my suggestion to incorporate this feature. I usually use IDTOligoAnalyzer Tool because of this: it's a complete analysis package despite the annoying need to create an account just to use their tool.

Another issue I've just noticed recently is the plugins section: almost all of the links posted lead to nowhere. I wanted to add a plugin to my UGene instalallation but was unable to because of it. Please fix the hyperlinks so they point to another web page where we can read about and download the plugin or alternatively begin downloading it right away.