In general migrating between version is a zero-impact job. I always try to make everything behave in a backwards way. There are new features and new things which pops in here and there but often it is not noticeable at all. There have been the odd breaking change in between version (for instance some performance data shifts) but often it is a changed feature and something which has to be accepted.
This however changes when we come to version 0.4.x as it is brand new internal "core" which means the the entire application had been rewritten and refactored to facilitate a more lightweight and powerful architecture. In general when it comes to 0.4.x it will still be backwards compatible but it is done so for legacy cases ie. when you do not want to take advantage of the new functionality.
As there is a lot of things which are new in 0.4.0 the recommendation is for most people to remain which the existing configuration and existing feature set to and thus not change anything! This so that we can stabilize the configuration migration before everyone starts to migrate. So if you are upgrading to 0.4.0 please don't change anything as of yet unless you are planning to do some manual changes.
If you still want to migrate (for instance if you need or want to use some of the new functionality) please review the migration guide for detail on how to do this.