Hi there,
The Indigo range is currently the only machine running a liquid ink system. This has the benefit of being able to more accuratly match Litho than any of the currently batch of toner based machines, including iGEN3.
Having worked on Xeikon 32/D, Indigo Turbostream and 3000/3050 products and more recently iGEN3 I am of the opinion that the HP3000 engine gives the best quality output, but not by much. iGEN3 has seriously brought Xerox back into the Digital Print market with impressive solid colours and bright vibrant images. I have only recently moved to the iGEN and we have had serious reliabilty issues with it which have hampered my experience with the machine.
If it was my money and I could only buy one press is would be the 3050 or 5000 (4000 if your wanting roll-to-roll), the quality of the prints and the option of using Indigochrome or customer specific spot colours in upto 7 station (6 in my opinion, 7th station is to unreliable due to the BID angle and the forces of gravity

).
As for ink changes on the Indigo its not to much of a problem. You can change most colours in under 15mins, 30 if you are going from a dark colour like reflex to a light one like yellow. Maintainance wise the machine is a little on the dirty side but if the Ops keep it clean and well oiled it won't cause any problems, also due to the fact it uses drums for image transfer and impression there are a lot more operator fixs and adjustments that can be done compaired to the iGEN which being almost completely electronic and requires specific engineer software to access a lot of the diagnostic DC routines.
If I could buy both then I would (I say both 'cos nxtpress is utter garbage). The Indigo and the iGEN would be an excellent duo, selling high coverage full colour work on the iGEN and playing to its strengths and running the jobs that aren't viable for litho or require more accurate colour matching on the Indigo.
Enough waffle,
Hope some of it makes sense.
ps. iGEN has a very clever spot colour handling system also (though the gamaet is limited) it will handle any colours on the page that are specified as spot colour indepenantly of the rest of the CMYK images. This means you can tweek the spot or the image and not bugger up the others colour ot tone. (we have a DocuSP rip so I aren't sure if this feature is available on the Creo Rip)