Performance-wise, they are going to be very similar, if not, exactly the same. So it's a wash.
Future expansion-wise, depending on what motherboard you have, it would be easier (but quite a lot more expensive) to add a second 690 versus a third/fourth 680 for added performance. Of course, this will depend highly on what resolution you are running how much you are willing to spend.
From a watercooling perspective, if you want better flow and lower restriction, then you would want less components in your loop. Therefore, the single 690 will be the better choice; although, it's really splitting hairs as most waterblocks today are not that restrictive anyway (including the Hydro's made by Swiftech for EVGA).
From a future selling point, the 690 would hold its value better than two 680's, although it may take longer to line up a potential buyer due to the higher price tag.
In the end, I would opt for whatever will be the easiest to option to obtain as both cards still readily go in and out of stock here in the US, so I assume it may be a similar situation for you as well.