Yes, graph is great! No other words!
About eqatations... I read your article at
http://www.brains-minds-media.org/archive/1411and, as i see from it, you are using your application in studing prosess in social studies. Am i write? I think it would be hard to explain to students java programming. So, it should be something simple. May be, something like Microsoft Equation.... Student select signs and operations from panel and fill its params.. But i think, it is hard to realize.
As for me (and, i think, many others) BeansShell and link to the langs syntax will be enough, but... One of project's goals is "Easy-to-use, visual GUI ... ets.". So, is it sutable?
May be this approach:
Step 1. Inserting BeansShell scripting in one version (may be 3.1) (small efforts, as i understand).
Step 2. In next (or next, next, ..., if the interest would be) insert any GUI, may be, like i proposed. This GUI will have button "Get script" wich will convert operations from panel into BeansShell script. (Support of scrips was realized in first step.) User could see this script and correct it, if need.