Fortunately my wish list isn't really very long. In fact, I only have two real items:
Full HTML browser within Flex
Today you can't really integrate HTML content into a Flex application. There are a few tricky solutions (mostly provided by floating an iframe on top of the Flash player). Unfortunately these have all kinds of problems. First, we have to change the wmode of the player for these to even work - and that immediately prevents screen readers from working. So enterprise applications where 508 compliance is required can't even contemplate these solutions. And even when we can use them, we're still stuck with other limitations as the actual HTML content is floating above our app and not really inside it.
To some people this might not seem like a very important feature request, but I've found quite the opposite. Every customer or potential customer I speak with runs into this. Portals/portlets are still all the rage (right or wrongly). Customers want a portal application where they can embed both HTML/JS portlets and Flash portlets. These customers have to choose HTML as their main platform (i.e. the container) rather than Flex. Other times, customers have an existing Java-based web app that they'd like to transition over to Flex. The keyword is transition. They can't just throw away their existing app and start over. They need to replace it bit by bit. But the architectures of Flex and the Web 1.0 world of these legacy Java web apps don't mix well. Ideally, they could rewrite the main frame of the application in Flex and pull in pages (say in a tab folder or something similar) of the old web app. Right now, thats not really feasible.
This is the #1 reason (in my experience) why organizations don't choose Flex.
Flex Compiler Performance Improvements
The Flex compiler is slooooow. Its been improved noticeably with Flex4. But its still too slow. On large projects its horrendously slow. This is one aspect where Flex and Flash Builder do not compare favorably with HTML/JS (obviously no compiling there) but also with Java or any other platform I've had recent experience with. I still believe developing with Flex, due to the productivity of the architecture, Actionscript language, and Flash Builder IDE is levels of magnitude better than AJAX. Yet, I can't stand the constant interruptions while I wait for the Flex compiler to finish. Fast is a feature!
To Adobe's credit, they do appear to be working on it. I just hope the work done in the Flex 4 cycle is the beginning and not the end of the improvements.
These two changes arise from the experience of Java developers moving to Flex - both my own experience, and what I've gleaned from talking to customers and their developers about moving to Flex. If Adobe resolves these, I think we'd see more Java developers happily using Flex in the future.