Open-source software gives a lot more ability to customize, build and troubleshoot when things go wrong. It also grants a level of clarity that Unity just doesn't have-as well as a lot more space. A Unity install can get quite large, whereas I can almost save Godot on a high-density 3in floppy if I really wanted to.
As a closed source project and with the recent controversy with Improbable, there's also good reason to have objections to using Unity-along with having no actual true 2D mode. While this has upsides, it also means you have some serious downsides.
Working with Unity gave me nothing but problems, despite the large community and its performance was poor. I found Godot and tried it. Quite zippy in performance.
The final consideration is the price. If a game I make with Unity went viral and sold enough, I'd have to pay a hefty price for a premium Unity subscription and royalties. If I make a game that sells well with Godot, the only things I need to worry about is paying the people I work with and taxes. It's a peace of mind I just don't have with Unity.
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I mostly agree with your points, and given unlimited time I would port to Godot and other engines, and even make a standalone version using .NET Core. However I do have to manage my time carefully as I have little of it to spare, and Unity seems to cover the most bases in terms of out of the box multi-platform support. Moreover, RetroBlit itself is not a free product ($15 USD as of this writing), so I don't think it fits well with the general free open source mindset. You do get the RetroBlit source code when you purchase it however.
As for Unity itself, there are no royalties at any level that I'm aware of. It's free up to $100k annual profit, and after that it's $40/year up for up to $200k, and $150/year for any amount beyond that (these are new numbers for upcoming cost changes in January). Personally I think that is very reasonable and I would not blink and eye at those costs if I was bringing in $100k+ from a viral game. You will in fact pay vastly more in store front royalties on most non-mobile platforms (Steam/Epic/Others).