Nexpress and iGen3 can co-exist. Especially with Prinergy in the mix. Prinergy can drive the DocuSP but you need some sort of Freeflow server in front of it, I believe. I am sure someone from Xerox can clarify, if not, I can get someone at Kodak to let me know.
I am fasinated by your take on the Indigo. I still suspected they have the problems they claim to have solved, but now I have some proof

Anyway, spend some time with the Prinergy guys, make sure you get a really good demo from the Vancouver guys via Webex.
I think you are going to find that Nexpress can do everything the iGen3 can do and more. But does that obsolete the iGen3? Probably not, you can make it work. I'd just worry what Xerox will do, if their service will drop off because of not getting that 2nd box.
You might want to throw out the possibility of taking out the iGen3 and putting 2 Nexpress in. Having 2 Nexpress is where the benefits of swapping parts and lowering costs really kick in. Just my two cents. Guess it depends on the age of the iGen3 and what is owed, etc. Be careful of the service contract cancel clause Xerox has though... Can be very expensive to cancel service. Make sure you time it right at your renewal stage if you think about doing it.
But honestly, Nexpress and iGen3 will be fine together. Prinergy is pretty much agnostic to output device support. The JDF stuff works just fine to DocuSP once translated by that Freeflow server part. Not sure if they send anything back via JMF or not, but that should come with time. Make sure you take a good hard look at the Nexstation vs the VCS rip on the Nexpress. Without having the PDF print engine now, you might want the VCS, unless you want the PDF Print engine (which I would) then the Nexstation is a must.
Good luck. Hopefully some others will chime in. I am sure Elmo will with his pro Xerox, buy 2 stance