Sorry for the challenge finding new replies to other replies instead of just new replies to the main thread. 

Those are all additional filters that need to be built up. Basically, when you reply to a post in the main body, it is easy to find it. 
However, when people post replies to other replies, that makes it more complex because those replies fall into a tree-structure.

To improve searching for "new replies" instead of just "new-posts" will require extra programming, probably, by me, if I find time.. 
There is lots of work behind the scenes like fighting spammers, balancing the memory, new users who fail to receive welcome mail (spam filters).

We even need an improved "drag-and-drop" photo filter which I have not tested. But I tested icons for GM-Level access so will deploy this weekend.

Programmers are expensive, so I do most of the work myself, hence, we can run this site on limited donations. 
Even Wizards of the Coast could not cope with needing to hire moderators, programmers, etc. ENWorld.org is doing great as an Indie, though!

Thanks for all your insights. Duly noted. 

I just had an idea. 

I can create a new tab that will filter every new reply, including "repleis-to-replies" in a list view.

That may help alleviate the pain and is a script I already used elsewhere so easy to deploy. 

Here is a new [tab] with link below (and in your forum tabs) that focuses on the new replies only.

Not an ideal solution, but the ideal one is too complex, and frankly, I may not have the time to test and keep the site stable.

http://www.7thsea2e.com/port/forum/replies

Alternatively, we may just follow @Salamanca's advice and remove the option to "reply-to-replies" and just default to "reply-to-threads"

I think the [replies] tab is fixed now as a clickable-list to all recent replies within their parent forum thread. Not a perfect solution, but hope this helps ease the frustration somewhat.

And thank you for your honest user feedback. It helps everyone focus on those things that improve the site, even in small ways.

With regards to major improvements that may require re-architecture, I am not sure if there is appetite for a funding round like a Kickstarter. We upgraded the servers through some "angel" supporter donations here.

Basically, we have done very well with very low budgets, so we will try to keep improvements within reason, which means not every suggestion can be implemented.

Once again, thank you all for the feedback.

For those who missed it, this was the ENWorld Kickstarter drive to upgrade their forums which I also helped fund 3 years ago.

https://www.kickstarter.com/projects/enworld/rebuilding-en-world

And ENWorld was instrumental in saving refugees from Wizards of the Coast.

Okay, the best solution we created on a limited budget requires a little smart navigation.

• Open the [replies] tab in a new window
• Look for a response you want to read and click on it. 
• Use the [Back] button of your standard Browser (Chrome, Edge, Firefox, Safari) to return to the list
• Look for another reponse you want to read and click on it.

NOTICE: If you do not use the Browser [Back] button, once you read one response in a forum thread, ths system assumes you read all repsosnes to that thread. 

Any further improvements will take too much time and time is money. 

I also added one more tab, that lists all "replies" within one day in most recent historic order.

http://www.7thsea2e.com/port/forum/rows

This continues listing those replies for the whole day, whether new or old.