The biggest problems with IE are ActiveX and the intimate connection between the browser and the OS.
I read somewhere, long ago, that the difference between Java(?, may have been something else) and ActiveX is that while both of them open the door of your computer to strangers, Java/whatever follows them around the house making sure they don't get up to no good, while ActiveX just stands at the door waiting for them to leave.
Having said that Java hasn't been faring too well recently in terms of security.
If I had to say one positive thing about ActiveX over Java, it is that at least you don't end up with all the compatibility issues with ActiveX.
At our place we have some applets that require a version of Java 6, they'll work with Java 7 but only if the security settings are changed. Then a different site comes along and requires Java 7 or early Java 8, then Java says "I need updating" and people do that and it breaks both sites as the later Java 8s require signed apps. And if they uninstall it then it goes back to Java 6 which breaks the second site.
Don't in any way get the idea that I like Java. I don't. And, as I think I've mentioned here before, I have to use an International regulatory database using Java that suffers from exactly the version incompatibilities that you mention.
bastard by name