I have no idea what your employer does with its time, but for most companies that prioritize making money, 3-4 years is a lifetime.
Plus, concidering the fact that JS differs from browser to browser (and most likely allways will), Flash has an advantage over JS: If it works on one client, it works on all others as well.
That makes for an easier (cheaper) production/testing cycle.

1. Current numbers point to a 96% adoption rate for Flash 6 and about 90% for Flash 7. I pretty much don’t hear the concern over end users having to install a plugin. In the media services industry its pretty much accepted that Flash is a viable way to go and most people have it. For a comparison, several sources say that Javascript penetration is also in the low 90-95% range. That’s pretty much the same as Flash.

http://www.macromedia.com/software/player_census/flashplayer/version_penetration.html

2. Can’t say much here. I guess it depends which apps you’re seeing. I wouldn’t generalize all Flash apps as being slow to load though.

3. Have you taken time to read all the accessibility features:

http://www.macromedia.com/resources/accessibility/

4. You don’t know how the developer built the swf. You can very much so seperate content and design. It’s all dependent on how the developer wishes to build his/her flash app. I’ve built apps that are completely OO oriented, are data driven and skinable via xml markup. Flash also supports CSS with its textfield styling. Many options here. Just because its delivered in a swf doesn’t mean the content, business logic and design isn’t seperate.

5. Not really sure what the point is, so I don’t know what to say but here goes: As a flash developer you can define whatever menu items you like in the right click context menu so if you’d like to put a “view source” option or a “save as” option, feel free. Many people in the opensource flash community are doing it now as a way of distributing source code.

Of course, there are plenty of other problems with flash:

1.) You have to install it. It doesn’t come with the browser.
2.) Most applications take a long time to load (this one doesn’t, but the developer is much better than most flash developers)
3.) Accessability is completely impossible.
4.) Design is tied to the swf file. So much for separation of content from design.
5.) Ever right-clicked a flash app? Yeah.

I don’t think anyone was ever really doubting flash’s ability as a front end. The whole POINT of the hype around Ajax and such is that they allow us to achieve flash-like things without flash’s shortcomings.