It's somewhat pointless unless you talk specifics. There needn't be any difference from a performance standpoint really. A "passive" sub will give you more choices of power, if that's important.
in theory the passive sub with external amp gives you more options in terms of upgrading for less money, and sub placement (if you had a room that is lacking in outlets).
Performance nod goes to the Ultra obviously (assuming it's well-powered), but convenience/features goes to the PC+.
If you wanted low-pass filtering, over-excursion support, subsonic filter, etc, w/ the Ultra, you'd have to get that Marchand box or something similar.
Personally, I like the powered route, if for no other reason than auto-on. With a separate amp, you'd have to either turn it on w/ the system or have it on some kind of delayed power switch like the higher end Monster Power units.
NHT did the subtwoi very well. the amp is built into the sub cabinet, but the crossover controls are not. thats a rack width component that has more adjustability and tunability than you can think of, and it sits in your component rack. Additionally, its a stereo unit, so you can have two cabinets and control them from one controller, running in stereo or mono, whichever you prefer.
Being a "gearhead," I prefer passive. That gives me a ready excuse to had more hardware to my rack – namely a big hulkin’ amp and an outboard crossover.
I vote for user-friendliness. Powered all the way. I prefer fewer components on my shelf. Saw a guy with shelves loaded with amps, laserdisc player, vcr, etc, and knew that was not the way to go. You want to have the right gear, but in the end, it's all about the show, not the gear. Besides, with a sub, you only need to set it up once and it's smooth sailing from there.
I have to agree with Wayne on this one, but I also build my own subs. I'd rather spend the money on a really high quality driver that can handle lots of power and then have an outboard amp. If I can't afford a huge amount of power in the beginning, it'll be much easier to upgrade the amp at a later time if it isn't bolted to the back of the box.