The VP6000 is Kenwood's high end single band portable, mainly aiming for the mission critical police and fire markets. It identical to the VP5000 but features a more rugged construction and a small top display. It's compatible with analog FM, Motorola Smartnet and Smartzone, and P25 phase 1 and 2. Programming is done using Armada.
The NX5000 is also single band but is marketed more for commercial applications. It's compatible with analog FM, NXDN, DMR, and P25 phase 1 and 2. Programming is done using KPG-D1.
For the protocols these radios have in common you more or less have the same set of features available with a few exceptions. As of now P25 two tone encode is only possible on the NX, but discounting that I'd consider the VP to be the better P25 radio. If you're only interested in analog the NX would probably be sufficient. Now as for programming softwares the two are entirely different beasts. Armada is fantastic if you're programming a lot of radios at once since it lets you move between multiple radios' codeplugs quickly and apply changes to multiple radios at once. It's also less finicky when it comes to radio firmwares; as long as Armada is newer than the radio's firmware, it will be able to read and write codeplugs to that radio. KPG-D1 works fine and is on par with other manufacturer's programming software, but it's nothing special.