well it depends on what approach you take to fixing existing problems. There are 2 ways to fix a problem, change the existing code to address the issue, or architect a new solution that not only eliminates the issue but provides much greater functionality and flexibility.
Let's look at the open "issues' that you're concerned about...
1. Search. As far as I can see, it's not a Repository issue, but a core search issue. That being my stance until proven wrong, I have no plans to change the Repository code to address this issue.
2. Permalink issues. When accessing an item through a permalink, the Comment count is zero. While this is not correct behavior, I wouldn't classify this as a critical issue. I'm not saying it won't be fixed, but I'm not going to stop working on 4.0 to address it.
3. Javascript. If a client has javascript disabled, much much more than the Repository is not going to work. So once again, I have no plans to change the Repository code to work if the client has disabled cookies or javascript
All of the source code is available. If any of the above items are critical for you, then you are more than welcome to make the code changes to address them. If you want to send me the code after you've changed it and tested it, I would be more than willing to incorporate the changes into a future 3.X release of the module. That's the whole point of 'open source' isn't it?
In the meantime, in order to respond to the first post in this thread, I am continuing to spend as much of my limited free time to work on 4.0. I am really excited about the progress I'm making, especially with the new template engine. I just finished the code that allows you to extend the template engine by creating Repository 'Controls' (.dlls) that you can then use within your templates. I will blog about my status and the new engine by the end of the week, including a brief demo of creating a new control and then using it within a template.