You seem to be ignoring the fact that Flash doesn't work properly on Linux, Android and iOS. Unless Adobe does something about it soon, Flash is going the way of the dodo.
It's nice for people to want their favorite Flash-based sites/games to work as-is on their phones and tablets, once you get down to it though, those sites/games just won't work well without major overhauls, and so instead of rewriting to Flash (with all its usability problems), why not give your users a better experience in a web-native or device-native form?
I'm using Linux myself full-time, but for flash games I might even consider Linux irrelevant if there is no way of getting good performance. The by far biggest part of the audience still uses windows and that probably won't change for quite a while.
Flash is installed outside the package management system (particularly on distros emphasizing Free Software: Debian, Ubuntu, etc.). This has improved through packaged installers (the plug-in's still fetched from outside of repos), but only in very recent times.
Flash content fails to load at all. I actually have this problem on several platforms, presumably because I limit JavaScript execution, and many sites now rely on third-party scripts for content generation (hello, Gawker, yes, you).
The player is very resource-heavy. I'll browse with several score tabs open. On a sufficiently beefy box, that's tenable, but with flash, memory and CPU utilization go through the roof.
The browser plug-in crashes, frequently requiring a browser restart to restore it. Given that Flash is virtually always at best ancillary to my browsing session (where I use it it's almost exclusively as a video player), my preference would be to have an external video player (I have several excellent free ones at my disposal). The crashes are addressed in Chrome as tabs and plug-ins run as separate threads/processes, but this still affects Firefox/Iceweasel.
There are numerous security and privacy issues with Flash, for which we're wholly dependent on Adobe to please, eventually, maybe address these.
64 bit Linux support was a long, long, long time in coming (and IIRC it's still weak). Until Linux itself got 32/64 bit library support sorted (again, only in recent years), this was a significant PITA.
Given Nielsen's criticisms (which address Flash as a website UI element, not such things as Flash video and games), yes, Flash is at least 99% bad. Most use is still advertising (yuk) and idiotic slideshows (infuriating). Its valid uses (videos, maybe games) would still be better addressed through standalone utilities rather than in-browser plug-ins, IMO. I use my browser for work and information, not entertainment. I keep a lot of state in my browser sessions, and they tend to live for days if not weeks.
All in all, as a Linux user, up until 2008/2009, Flash was sufficiently a pain in the ass that I'd generally just not bother installing it. I install it now (it's gotten easy enough) but block the hell out of it, with my rare use-case being YouTube videos and the very occasional informational graphic which makes valid use of Flash.