I like how you approach your problems with Basecamp as usability issues and not as feature-set limitations. I think Basecamp is at a sweet-spot with features, but has a lot of room for improvement in how users interface with it. The application really hasn't changed much since it was launched. With the mountains of data on how its used, I would think 37signals would refine the app to be the most usable interface in the world.
My (rejected) YC project literally addressed every single concern voiced in this article.<p>If you can relate to the struggles of managing and working in multi-resource, multi-project environments, sign up for the beta of FlowRocket at: <a href="http://signup.flowrocket.com" rel="nofollow">http://signup.flowrocket.com</a>.
I'd recommend checking out <a href="https://www.greplin.com" rel="nofollow">https://www.greplin.com</a> to help search basecamp. I've encountered some of the same issues with their search you have and Greplin makes things much better!<p>(full disclosure: I work at Greplin ;-)).