The PM's should definitely not go completely bye-bye.....
Folders would be good. Also good is the SI "who wrote" feature...where if you call up a PM it is responding to Member X (who wrote) and you keep clicking back through the "who wrotes" to get to the beginning of the conversation. I find that really useful sometimes.
As for ads, I may be in the minority here, but I hope to see ads all the time. I want the site to make money. Even lots of money. The only restrictions I would place on that are the following:
1. Don't hog bandwidth. In my neighborhood, high speed Net access is not available....so if you put some fancy graphics-laden ads on the site it's a PITA.
2. Don't mix them into the text of the messages at all, even in a different font etc. It can make it look like there is some connection between the message and the ad. I know Cousin Shorty (who may not have found his way here from the home planet yet) feels very strongly about this. So do I.
3. As the site adds more features, like quotes and charts and news and stuff, it is better to place the ads there if possible than in the messages themselves. Though I don't mind something unobtrusive in the messages.
I think a lot of people here don't want to see ads at all. But we have to be realistic. Matt started this site as a business. He could have joined the Peace Corps instead. Ads are one of the main ways to make that business make money. One of the only other ways is to reach into my pocket, and I'd prefer you didn't do that. Even if you grandfather people in and start charging, the minute you start charging the community might as well be closed. Those days are gone, probably forever.