Chrome and Safari are both based on Webkit, and Webkit is opensource, so many of the improvements made for chrome will go back into Webkit, and therefore Safari.
The problem with Flash, is that it still requires another program to operate, Chrome uses the plugins already used on IE to process Flash, and JAVA support has nothing to do with browsers, but the system/OS.
So no, there will be no Flash, until Adobe/Apple develop a plug-in for the iPhone, and JAVA likely will never come because it would need to be integrated with the OS.
Also, don't confuse JAVA with Javascript, while the names are similar they are completely different and incompatible technologies, and Safari for the iPhone handles the latter just fine.
TEG