As for the performance and maintenance differences between Websphere and WLS - I don't think there really are any. JDE is really the "lower" common denominator - and neither Websphere or WLS are being truly taken advantage of by JDE code.
WLS is the direction for Fusion Middleware - so if you are implementing integration using FMW or Oracle SOA Suite - then you'll be utilizing WLS no matter what.
Also - if you are using Agile/Primavera/Demantra or any other Oracle owned product - theres a very, very good chance that you'll have to implement WLS for those too. Even Oracle Application Testing Suite uses WLS.
BUT - are you licensed for it ?! Websphere is a part of the blue stack, and if you have the old Technology Foundation "blue stack" - you need to upgrade (blue stack expired). If you own Websphere licenses and not bluestack - then switching to WLS might be a very expensive proposition.
Oracle Technology Foundation can be a very expensive option if you don't already own it. Check with your friendly Oracle representative...