This partly depends on the version of MATLAB you are using as App Designer has seen large improvements in recent releases. If App Designer supports what you need, use it instead of GUIDE. A few reasons:
- MathWorks is no longer putting development effort into improving GUIDE, and hasn't for several years. Meanwhile a significant development effort is going into improving App Designer.
- App Designer looks much better and is easier to use than GUIDE.
- As of R2017b, App Designer can pretty much do anything GUIDE can do.
As for packaging MATLAB Apps, any interactive GUI can be packaged as an App, whether it was created with GUIDE, App Designer or manually from scratch.