Frequently in a thread it becomes difficult to determine who the respondent is replying to.

The way that is commonly solved is by providing a little link that points back to the original post. One of the cleanest is Amazon's forum that shows a little popup showing the linked post's content.

Additionally, besides the reply & quoted reply there could also be a reply link that is not directly replying to any specific post but instead the topic.

Normally posts are sequential, but not always. Not a big deal, but sometimes it does get confusing

Sounds sensible to me. I think we are focusing our development efforts at this time more on improving major system components rather than making feature tweaks, but I'll add this to the list of good ideas for consideration.