Some suggestions I think would improve navigation a bit:

1.Comment votes. I think comment votes should appear at the bottom of the comment. The reason for that is is to avoid "copycat voting" (I'm sure there must be another term). I think it's a common effect: you see a comment, you see it has 5 votes while the rest you've been reading have 1 or 2, you start being predisposed to see it as a valuable comment even before reading it, you end up voting it too, etc. Similarly to why the top level reply box is at the end of the thread, I think having comment votes at the end of the comment (or even hidden under an expandable menu, but maybe that's too much) would help users reading comments more open-mindedly. I would even argue that putting the user name at the bottom would be a good idea as well, especially since the user base now is small is easy to adscribe more credibility to some user names than others, which is not bad by itself, but might push a type of "authoritative bias".

2.Top level comments count. If we understand top level comments as the main ideas discussed in a thread, maybe it would make sense to show that in the post. Right now, what we get in the submission listing is the title, username, the ~, the tags and the comment number. I wonder how important is having the total comment number shown here. I guess it's an indicator of activity, but maybe it'd be more interesting having the top level comment number, indicating the ramifications of the topic. Total comment count could be maintained as well, or not, or just when entering the submission, etc. New comments could still be shown in the listing. After all, if we are ordering by activity, we care that there is some activity, and total number of comments is not that relevant.

3.Cascading tags. Not so sure about this one, but I though I'd mention it. When marking a comment Off-topic... I think most usually all comments under that one will also be Off-topic. Maybe it'd make sense that from that point on all comments would be marked as off topic automatically, and possibly collapsed. Right now it seems when there is an off topic comment thread, you just keep seeing off topic tags down the line, which is a bit distracting and probably unnecessary since they are almost surely going to be off topic, so it's probably not necessary for user to try and judge that. Maybe, if it makes sense, this would better be done when the tags are more developed.

4.Parent link for context. Thank you for adding the parent link! Much needed. However, wouldnt it be better if when tapping a parent link, the end page would be the parent comment (obviously) plus the comment where you tapped the link? What I mean is, to provide better context, I think it'd be better to show the parent and the comment I was reading, with all other comments under the parent AND above the origin comment collapsed. I don't know if that's clear...

5. Reply - Tag - Vote. Probably a bit nitpicking here, but I think inverting the current order of the Reply and Vote buttons would be a better fit. Since most people are right handed, and the action of voting is (probably?) more common than replying, having the vote button on the right side might be a minor enhancement in usability.

6.Highlighting OP's comments. Right now, OP's comments are marked by "(OP)" next to the username. I think it'd be better to make the indication more evident. For example, displaying OP's username in a different color or marking the comment with a different color (as with new comments in orange or own comments in purple). I would prefer the username color since it's less invasive while still being easy to spot.

Anyway, just some ideas I've had in the last few days, hopefully not too ridiculous or confusingly worded.

EDIT: Sorry for the generic title, I forgot to edit it before sending...