Noticed the "p.s." part? I asked for specific parts of the Flash apps that can't be customised - tell us, we'll get them fixed, so that it would all be customisable. It would still have to be done using current method - firing up Flash and changing the FLA files. Later today we'll also discuss changing Flash templates along with the site templates to adress the kind of problem that you sampled on your site.
As for switching over to the templating method that you suggest, that would be see more counter-productive and would take about as much time as development of a new non-Flash chat and IM. We'll try to push the new apps to happen sooner than a year.
As for switching over to the templating method that you suggest, that would be see more