They really are almost identical areas, except for a few minor things.
Lower Macungie is a bit more developed than Upper Macungie, but not by much. Lower Macungie also contains the very quaint town of Macungie.
Lower Macungie is East Penn School District, Upper Macungie is Parkland School District. They are both very good districts. I do believe that Parklands school tax might be a bit higher than E. Penn. Parkland is paying off a mega high school complex that they recently built. I had kids in Parkland and only have good things to say about it.
Crime is not a problem in either area, housing costs are about the same.
It really depends on if you want to be in particular school district or in an area that is a bit less developed.
I do believe that Upper Macungie has a great park system and has a few more than lower Macungie. Here are links you might find helpful.
http://www.uppermac.org/index.html
http://www.lowermac.org/
http://www.parklandsd.org/index.php
http://www.eastpenn.k12.pa.us/index.php