There's a lot to cover here ... and replying to this will, at the very least, help me to organize my thoughts and is a good opportunity to broadcast what I've been thinking and planning for Paint.NET's future. What you've discussed is many years worth of work, by the way. Patience will be needed. And I don't necessarily agree with everything ?
The website screams 2007 because I made it in ... 2005 or 2006. I'm not a web developer As @Ego Eram Reputo mentions, there's a new design that is awaiting my attention. It's very high up on the list, and will probably be what I tackle once 4.1.1 is out the door. The Windows Store is also a really great place to get Paint.NET now. There's a 30-day trial and then it's a few dollars, and it's always up-to-date and whatnot. If you want to recommend Paint.NET to a friend, I would like to recommend to you to recommend this approach It used to take an entire week for me to push out an update due to Microsoft's lengthy certification process, but 4.1 was approved in about an hour (which is a really big deal!), which means several weeks per year of wasted time is no longer an issue.
Here are some more of my thoughts on Classic vs. Store: https://blog.getpaint.net/2018/01/14/paint-net-4-0-21-is-now-available/#comment-9811
I personally think the UI icons still look quite good and pleasant, and I'm okay with them compared to the amount of effort it takes to update them. Well, maybe the better way to put it is that I'm less worried about the styling and much more worried about the resolution. Thankfully, there is already some preliminary progress being made here thanks to @Zagna: https://forums.getpaint.net/topic/111729-high-res-icons/ . And, since the whole icon set needs to be redone to support higher resolution, the styling may get a ride too, probably to mimic the latest Office style. However, don't load up on the expectation that Paint.NET's icon set is always going to be following the latest fashions. It's just an obscene amount of work, it can only be done so often.
There are more updates planned for improving Paint.NET's support for high-DPI. WinForms was finally updated to support multi-monitor mixed-DPI, so I'm hoping to get Paint.NET hooked into that as well. High-DPI is something that I've been chipping away at steadily for the last few years. Just look at the roadmap and search for "DPI".
I would not expect a radical departure from the current set of UI components, like you called out on the Colors form. Standard Win32 controls work, and the only reason I'd depart from them is if I were to rewrite everything in a new UI framework. I would not place any bets on that happening. It would be an insane amount of work for a very small subjective gain.
Lack of tools, as you put it, will be chipped away at as time goes on. Flip Horizontal/Vertical should be straightforward. Some of the others are available as plugins. You don't define what you mean by "Align" and "Mask" so I can't really comment on them. The plugin system itself needs a lot of upgrades; in 4.1 I unfortunately had to block the Content-Aware Resize and Bulk Updater plugins because of how they forcefully integrate themselves via reflection. I can't really take offense at what they had to do to accomplish their goals; I'd really prefer to make a plugin system that provides them what they need.
And, of course, BRUSHES. This should be a rich staple of an app like Paint.NET, and it's not, and it continues to eat at me. The brush system was completely redone for 4.0 but there wasn't much in the way of new functionality for the user (largely because at that point 4.0 was a 5 year project and I was exhausted and needed to ship it). This has been at the top of my list since 4.0's release but I've never had the time to tackle it. More on the time aspect in the next few paragraphs. Suffice to say, things will be coming: more built-in brush types, official custom brush support, pen/stylus and pressure sensitivity support, etc. This is all towards the top of the list. Smoother drawing, of the type you specifically call out, was attempted in 4.0 but only got as far as using the GetMouseMovePointsEx API in order to get a higher sampling rate on the input (which, as it turns out, is buggy since Windows 8, hence the "Fluid mouse input" option for troubleshooting purposes).
All of these things have to be prioritized and interleaved along with other work. Crashes and bugs are always a high priority. New functionality has to be weighed with what it adds now, versus what it might complicate further down the road, or if it would be a lot easier once other foundations are in place. Larger work items, like GPU-enabled effects or major upgrades to brushes, can take a few months worth of work. As such, there's only room for a few of those per year.
Paint.NET has long suffered from insufficient development resources. As the app has aged, the amount of incomplete modernization work has also piled up. You mention a lot of things that need attention, but you forgot to point out where progress has been made! The Windows Store release was a huge effort, as was the dark theme and other high-DPI work that shipped at the very beginning of this year. There will be continued progress on this front, but don't expect v4.2 to come out and magically fix every last thing. It will tackle some modernization, it will tackle as many bugs and crashes as are needed, it will include some small features, and hopefully 1 or 2 big features. Just like 4.1 did.
Also, I think Paint.NET has held up better than most other 14 year old Windows apps that are maintained by small dev shops. I do take this stuff seriously!
Lastly, things have improved dramatically on the "time" front this year. I've opened up the private GitHub repo to a few trusted individuals and they have started chipping away at some things (see the change log for 4.1), which is already saving me time and benefitting the user base. I've also been able to allocate much more time to Paint.NET since I left my job* at Facebook in March. This is why 4.1 was able to include the upgrade to Direct2D v1.1 and the GPU effects: there's actually A LOT that changed under the hood, much more than you might think as "just" a user. Not all of that work was specific to enabling GPU effects, but it will pay dividends in other ways in the near term.
* yes, this is the first I've publicly mentioned this ... I decided become a "free agent" for now. I'm not working "full time" on Paint.NET, but that's just splitting hairs with the calendar. It is currently the only thing I'm working on, and so it's getting something like 3-5x as much attention as it was before.