Since your question probably doesn't have an objective answer, I'll chime in with my speculations.
Personally, I'm not even sure rJava specifically is the problem. To me it seems more like Java itself is always breaking in subtle ways that require a bit of CLI voodoo to bring it back to life. Once you can make Java work properly 9 times out of 10 the sudo R CMD javareconf makes sure that rJava works without issues.
And given that there are so many issues with Java, I'd say it's no wonder that odbc is recommended over JDBC. I'm one of those people who would always recommend to first try doing whatever you are doing with odbc and only if it doesn't work for some reason to try and make rJava work.