For those who cannot choose between the two, here are some of the differences: (these are only based on diffing the files inside the two ROM, no actual flashing was done. If someone has some better comparisons, feel free to post them)

kernel:
The size of both decompressed kernel are the same, the initramfs part is actually identical (except the order of the files). Inside the decompressed kernel there are a lot of 1-byte length parts that are different, but only 3 major chunks that are quite different.

The first of these chunks is the cpio's initramfs part, which is actually identical at the file level, but the files are in a separate order inside the cpio archive, that!s why the difference.

The other two chunks (around 0x75F90A and 0xA68F5D) are probably some part of the kernel don't know which part, and what they actually do.

Conclusion: although there are differences, the two kernels seem to be mainly the same, their decompressed sizes are actually equal, and the initramfs part is the same too.

CSC

The JPM variant has the usual multi-CSC's: CPW,DBT,KOR,XEO,XEU, and nothing else
The JP6 variant has only one CSC: XEE (nordic), but features Swype with 14 languages.

Conclusion: the CSC part with the added languages for swype is better in the JP6 variant.

FactoryFS
I only did a diff if the file sizes are different. The following files are changed:
- build.prop

- almost all files inside /system/app (minimal changes in filesize (few bytes), probably only because of signature changes except for Maps, Emaill, Gmail, DialerTabActivity, and the followings)
- AxT9IME is much larger in JPM (probably more languages(?))
- Swype is much larger in JP6 (and JP6 has a separate swype inside the CSC too)
- flash_player is larger in JP6
- VoiceSearch is much larger in JP6

- NOTICE.html.gz

- almost all files inside /framework, but only a few bytes changed, except for framework-res.apk. framework-res.apk is much larger in JP6

- libSwypecore.so and libXt9Core.so. libXt9core.so is much-much larger in JPM!
- libspeech.so is only in JPM. libvoicesearch,so is only in JP6

Conclusion: JPM seems to have a better xT9 support, but JP6 seems to have newer applications (if newer means larger...)