They are a totally different thing. Very little comparison is possible, really:
* PRS+ is based on the original Sony firmware, focusing on fixes that can be done through modification of internal files: directories support, extra applications, dictionaries, better (more detailed, anyway) keyboard control... The rendering engine is unchanged.
* EbookApplications is a brand new firmware which has very little to do with the original firmware. As such, it doesn't have its shortcomings (e.g. the long "prepare" time when the device is disconnected from USB), but also its good features (e.g. LRF support is gone). My major problem with EbookApplications is that it is in VERY EARLY stages of development and as such lacks a lot of features I consider a must (e.g. the ability to actually format e-books, with headers being rendered in different size font than body text). IF that is fixed sometime, it MAY become a viable replacement of the original firmware (and PRS+), but so far, if you want to read something better than mere plaintext files, you are pretty much out of luck with this firmware.
At the moment, I would say stay away from EbookApplications, unless you are a would-be Reader hacker - the firmware may not be usable for actual reading, but it is an AMAZING leap forward in terms of what's possible to do with your Reader and it opens some great possibilities in the future.