I use original WTP from eclipse.org.
As I install new version of JBossIDE almost everytime I have to remove encapsulated WTP components and replace with original WTP manually, because, naturally, original WTP appears to be newer (and sometimes stable).
It would be nice to have a release of JBossIDE, which references WTP (e.g. in requires section of feature.xml) instead of encapsulating it.
Removing WTP jars would also make JBossIDE ZIP itself substantly smaller.