Here's what I would have done.
Keep the main page on each board the same as it is now, except instead I think you could fit more topics in the same amount of space.
When you click on a topic, you then get a page that shows you an overview of that whole thread, similar to the old Chowhound (but only that thread).
You can then click on the post you want to read and it's there (providing that you can be sent to the correct place in the next page). 2 clicks, no scrolling, and you've reached the post you want. Under the present system, scrolling through an entire thread EVERY TIME is an awful waste of time.
This keeps all of the advantages of the old system: Seeing slight topic changes, keeping subthreads, etc. In many cases, seeing an overview of the thread (like the old Chowhound) saves you from having to read a post or reply you don't really care about.
The big advantage of this over the old system: no long pages to load, the topics are kept fresher, and no scrolling.
Scrolling is evil.