Isn't this simply the cornerstone of functional testing?
At that level your tests should be executing business test cases. If a functional test fails there is either a corresponding unit test failure or the failure of the interaction between the methods rolled up into the business logic (functional test).
Agreed. I'd like to know the numbers on how much users are willing to pay for an application such as this. Having this metrics helps to determine the quantity/size of features in the application.
Example, enterprise applications are loaded with features and have a much higher price point. On the other side, there are may free applications out there that are much more lightweight.
Which market you choose to target helps determine the price point. That price point will drive the selection of features that go into the product.
Is your goal to run this as a business? If it is you're asking the wrong question.
"What kind of note taking software would you build?" is a question a developer/engineer asks.
When you put your business hat on you need to start asking questions such as "What kid of note taking software would you pay for?" & "How much would you pay for note taking software that does X?"
If your goal is a business & not a hobby (which I assume it is since most people don't borrow 50k for a hobby) you need start asking questions related to generating revenue. You can build the best note taking software ever but if no one is willing to pay for it it will not be a profitable business.
Fortunately (or unfortunately) the reason these pop-overs are still used is because they still work.
Users are much more likely to perform an action (ex. subscribe to a mailing list) when it is presented to them in a pop-over. (At least that is what my experiences have been)
If you hate them or not, they do work and until the numbers prove otherwise site owners will continue to use them. The decision purely comes down to the best way to increase key metrics.
In full disclosure - I am the founder of http://RateMyStartup.com - The site lists new starts (and uses pop-overs). I would recommend checking out Nevahold.com directly to give it a chance. It really is a cool concept for a startup.
I'd like to see more on the main page about pricing. You mentioned "Both the core service and the monitoring agent will be Free Software" but is there a charge for the service?
On a side note... This is a great idea, I am the founder of http://ratemystartup.com - If you would like to submit your startup there I should be able to get you up on the site quickly.
tl;dr - The better solution is probably no public loans or grants whatsoever.