I think Apple is right. Flash is on its way out. Apple has a history of quickly moving to the latest and greatest, especially at the cost of breaking backwards compatibility.

One of the advantages of moving away from Flash: security issues. Quote from the US-CERT mailing list:

National Cyber Alert System

Technical Cyber Security Alert TA10-162A

Adobe Flash and AIR Vulnerabilities

Original release date: June 11, 2010
Last revised: –
Source: US-CERT

Systems Affected

* Adobe Flash Player 10.0.45.2 and earlier 10.x versions
* Adobe Flash Player 9.0.262 and earlier 9.x versions
* Adobe AIR 1.5.3.9130 and earlier versions

Other Adobe products that support Flash may also be vulnerable.

Overview

According to Adobe Security Bulletin APSB10-14, there are
vulnerabilities in Adobe Flash and AIR. These vulnerabilities
affect Flash Player, AIR, and possibly other products that support
Flash. A remote attacker could exploit these vulnerabilities to
execute arbitrary code.

I. Description

Adobe Security Bulletin APSB10-14 describes vulnerabilities in
Adobe Flash that affects Flash Player and AIR. It may also affect
other products that independently support Flash, such as Adobe
Reader, Acrobat, Photoshop, Photoshop Lightroom, Freehand MX, and
Fireworks.

An attacker could exploit these vulnerabilities by convincing a
user to open specially crafted Flash content. Flash content is
commonly hosted on a web page, but it can also be embedded in a PDF
and other documents or provided as a stand-alone file.

One of these vulnerabilities, CVE-2010-1297, is being exploited
against Flash Player, Adobe Reader, and Acrobat. Additional
information about CVE-2010-1297 is available in US-CERT Technical
Cyber Security Alert TA10-159A and US-CERT Vulnerability Note
VU#486225.

II. Impact

If a user opens specially crafted Flash content, a remote attacker
may be able to execute arbitrary code.

III. Solution

Update Flash and AIR

Adobe Security Bulletin APSB10-14 recommends updating to Flash
Player 10.1.53.64 or 9.0.277.0 and AIR to 2.0.2.12610. This will
update the Flash web browser plug-in and ActiveX control and AIR,
but will not update Flash support in Adobe Reader, Acrobat, or
other products.

To reduce your exposure to these and other Flash vulnerabilities,
consider the following mitigation technique.

Disable Flash in your web browser

Uninstall Flash or restrict which sites are allowed to run Flash.
To the extent possible, only run trusted Flash content on trusted
domains. For more information, see Securing Your Web Browser.