Hi, I don't have extensive experience, but I've had a Hunter 44DS 2007 for a little over a year now. It has needed a lot of deferred maintenance taken care of, but all of the "bones" of the boat have been great. I haven't found anything that I'd consider a build defect. The gel coat cracking is the closest, but that is clearly visible and just cosmetic.
One big feature that the Hunters tend to have is a Generator. Most Junneau's apparently don't come with that standard. It can be quite expensive to retrofit. Being able to run the air conditioning when off the dock can be a life changer, depending on how you plan to use the boat.
I did have lots of trouble with the furling main sail, but that turned out to be due to the foil tension being way too loose. I tried everything else first because the descriptions of adjusting that in the manuals was really confusing and intimidating, but adjusting it wasn't really hard in practice.
Hope that helps.