Which one is better and in what way because I do use FindBugs, PMD reports and CheckStyles plugins along with code coverage plugin. If anyone could guide me please let me know.
The latest version is almost always the better one. But you can try yourself. You can have as many different eclipse versions installed as you like. So grab a 3.6, add your plugins and enjoy the advantages.
Your plugins should run in 3.6 and if you encounter problems, I'm pretty sure there are updated versions available already.
If you already use Eclipse 3.4 and have a functional working environment and is pleased with it, then stay with that since a lot of small things change from release to release.
There is a lot of new facilities which may be interesting to you, but not necessarily anything warranting an upgrade. You can have a 3.6 installation next to a 3.4 installation without any problems so you can try it out, while being productive in 3.4.