Its not impossible, but there are not many applications that support OpenType glyph substitution. Word 2010 will and InDesign or Quark Express. I think PhotoShop does too.
It is possible to set up automatic glyph substitutions so that if you type ae what you get is æ — the same principle can be used to get glyph variants of a, depending on which letter follows it. It is also possible to use the Randomize OpenType tag, though I have never done it. Prepare yourself for some serious study.
FontCreator doesn’t yet offer any way to add OpenType features, primarily because of the dearth of application support, but it is not particularly hard to do with free 3rd party programs like VOLT or OpenType Compiler.