I'd go for the Vita-2000 if you prefer more natural colours. I'll repost what I said before about the display:
The LCD is better. OLED tech has come a long way since Vita's second gen Super AMOLED Plus panel, which is equivalent to what was in the Galaxy S II, so oversaturated colours, an inaccurate white point (whites look like blues), screen grain/Mura and burn-in. The OLEDs of today, like in the Galaxy Note 4, have caught up with LCDs where they fell behind before, but the one in Vita-1000 just isn't great by today's standards and is certainly a first/second generation product.
Here's a quantitative analysis of the Vita-1000 display, you can see it doesn't produce natural colours, has a white point that's completely off the charts and very low brightness of 117 nits. Today's smartphones hover around 600 nits. Bear in mind that that display review was from 2012, and things have moved on even further since then. What was once an impressive display just isn't anymore.
By comparison Vita-2000's LCD display produces much more accurate colours (a subjective comparison with my iPhone 5s shows they are very similar, the the iPhone 5s display is well calibrated), very good viewing angles and it's brighter outdoors. My only criticism with it is that the backlighting is uneven along the bottom, which is noticeable when the screen's displaying white colours. Also, it would be nice if Sony bonded the glass with the screen itself, something I wish Nintendo did with the New 3DS XL (which itself has a much improved screen over the old 3DS XL)
Of course, whether you'll miss the OLED display of the original depends on whether you prefer oversaturated colours to natural ones. I prefer seeing my games as designers intended them -- especially the many ports -- so I really like the Vita-2000's display.
The colour difference isn't down to whether it's OLED or LCD at all, rather it's down to Sony calibrating Vita-2000's display better. It would be nice if Sony pushed out an update that allowed us to choose colour calibration for the original model. Nokia did the same for their Lumia smartphones -- I had a Lumia 820 and while its OLED display shipped with oversaturated colours, an update allowed me to select a calibration setting that made it display natural colours.