The original author of this plugin, David Artiss, worked closely with WordPress advising them on a change to the WordPress Core to improve transient housekeeping.
However, it didn't go to plan.
A number of plugin authors use transients incorrectly, relying them for storage of data. Basically, if the data is housekept it will cause problems - this is NOT how transients are meant to be used. However, WordPress decided they didn't want to make a change that could potentially break some people's installation so made only a minor change for 3.7. This change clears down transients whenever a database upgrade occurs - just one part of the functionality of this plugin (which now, can be removed - expect an update to do this in due course!).
Therefore, for proper transient cleaning, this plugin is still absolutely relevant. If you come across a plugin that this causes to break please let us know - however, we are currently not aware of any.