Well the bigger worry is that more publishers will now take action as well. They see that it works now.

For a company that have so many ways they sell their older games, Im kinda surprised they are.

Nintendo should have had the virtual console up well over a year ago but at the same time I have no sympathy for rom sites

It's quite likely that they have nowhere near that.  The amount doesn't really matter as long as it's enough to ruin the accused.  It's possible that they'll declare bankruptcy and Nintendo will take much less than that, perhaps even a fraction of the total.  Everyone involved would be aware of that when the settlement was proposed. 

The point is really to send a message that they are willing to destroy someone's life over this.  

That's the part that I hate, that they're claiming this "caused Nintendo irreparable injury."  I would have been okay with it if the settlement had been simply to close down the website forever plus the seizure of all assets used in its operation.   

Terrible analogy.  If a car is stolen, then the owner loses the use of that car, plus any ability to sell it or make a profit on it in any way.  A better analogy would be if someone started making replicas without permission.  

This has nothing to do with game preservation.  Nintendo is protecting the rights to their own IPs.  And yes, people still do make money off 15+ year old games.  See NES Classic, SNES Classic, Flashback Consoles, previous iterations of Virtual Console, etc.  Nintendo, and @Games did go through the trouble of making sure they went through the proper licensing channels to put games on those systems for a reason.  If the ROM sites were these altruistic, philanthropic entities selflessly concerned only with preserving niches games that aren't available in the wild that you make them out to be; there wouldn't have been any Nintendo IP's on those sites in the first place.  And then, Nintendo wouldn't have a case against them.  

Should we also fret over the life of a bank robber being ruined when they get caught?  Whose fault is it that they chose not to make an honest living?  There are risks involved when you decide to take short-cuts in life by profiting off of things you have no legal right to.

Are you doing bad analogies on purpose or something?  

They agreed to pay it, which makes one wonder how much they were profiting from the ad revenue.  You have seen the potential on YouTube before their new policy changes.

Free to download or not, they were still profiting off of Nintendo's IPs.

1. Providing a service like this is kinda asking for trouble, especially if you make money on it through ads or other means. That said...

2. I don't think it makes a difference legally (could of course differ from nation to nation) but when games aren't actually sold anywhere (and no, I don't count the second hand market) then I personally have no issues with sites providing roms or iso's for those games. If the maker wants to continue to make money on those titles they should make them available for purchase.

3. 12 million is overkill.

Are you purposely ignoring the point that someone took a shortcut in life to profit off of someone else's property and got caught?  When you use someone else's property to try and make a profit for yourself, the repercussions of getting caught are yours to deal with.  No reason to lament that.