I love speculation. since this thread was made before portal 2's release, i'll share what my thoughts were back then:
The plot is that chell wakes up in a room, and the room automatically gets her to the test. she later meets wheatley and they try to escape, meeting some of wheatley's friends along the way. but wheatley is killed by glados when she turns on. glados sends chell through testing, every so often sending her into bts areas to get one of wheatley's core friends and return it to glados. glados takes the entire game to repair the whole facility, and is very nearly done when chell finds a morality core and gives it to glados, who installs it. big epic boss fight where chell actually damages glados as apposed to un-installing components, and chell escapes through a hole that opens when glados is defeated. one thing missing from the final product that i enjoyed in this speculation is the exploration in bts that i expected to see a lot of.