HTML5 is on for the replacer role, but Flipline guys won't be capable of rewriting their data onto HTML5 or so. However, I do hope so too.
This, or for Oracle's Java to step up. There are games I play that require Java instead of Flash, maybe because they need to be downloaded I guess
As Java developer I must say, that apart from Minecraft, there are almost no significant games, that are written in Java, Java is mostly used for business applications. Java plugins for web browsers are not supported anymore (only IE supports at the moment), as applets (Java applications for web) where very nasty and not safe (I worked using them, so I know what I'm saying).
Maybe you meant JavaScript, which is not related to Java. Then I think it's not a problem, JavaScript is very widely used in any web applications.
And about HTML5 games. Those are not written directly in HTML, as HTML is only markup language, that says what's on the page. Games are rather written in JavaScript, and then using HTML inserted into page.