I'd personally avoid the 3-speed as it has the weight of the 6-speed in combination with a gear-range not much more than the two-speed: the worst of both worlds. Also 2013 brought changes that were useful: better rims, JIS bottom bracket with interchangable chainwheel, better brake-levers. So the more expensive one would be clearly worth a higher price for me. 1000$ for a 2015 6-speed seems to be a fair price but I do not know the US-market and it depends on if it has a light or rack and if the bars are the version of your choice.

If you want to convert the bike to 8-speed you have the choice between the S/A XRF8w, the Shimano Nexus, the Nexus premium and the Alfine-8. Any of these conversions adds about 1kg on top of the weight of a 6-speed and offer about the same gear-range as the 6-speed (the S/A slightly more) but with finer steps (as they have two more gears within the same range). The main advantage is a more comfortable way of shifting. If you have to carry your bike a lot it is worth thinking about if this is worth a kilogram of weight.

The XRF8w can be brought down to about 112mm OLD, thus no need to modify the rear frame. You have to modify the chain-tensioner a bit but this is not really difficult. The Alfine-8 needs 135mm and can AFAIK not be brought to a lower old. Therefor I'd avoid it - it does not offer an advantage over the Nexus Premium but you'd either have to spread the rear-frame massively or to exchange the rear frame and in this case you can go for the rohloff or an alfine-11.

The two Nexus-models can be brought down to about 123mm OLD, spreading of the rear frame is necessary but within reasonable limits. Still a non reversible modification. The Nexus premium is of higher quality than the Nexus, so the choice between the two is a no brainer. The hub has to be modified including the cog has to be made a bit slimmer. The modification can be done at home but you'll need skills and a bit of trial and error.

So from the "do it yourself"-perspective the Xrf-8 seems the most attractive option, the more as you simply can buy a kit a kinetics/Ben Cooper. However: I own two XRF8w and would not recommend it in comparison to the Nexus 8 premium for a number of reasons - I have outlined them recently in another thread here in the forum.
The five-gear SRF5w seems attractive, too and I know someone who is really happy with it. Weightwise in the same ballpark as the 6-speed but with a single shifter. Too bad it has huge gear steps and a smaller range - basically it is a 3-speed with 2 more gears.

rangewise:

133% 2-speed
176% 3-speed
256% 5-speed S/A SRF5w
302% 6-speed BWR
306% 8-speed Shimano
325% 8-speed S/A XRF8w

I did not like the XRF8w for various reasons and did not like the 8-speed shimano for weight, price and modification of the rear-frame. The 6-speed has huge gear steps. Too bad. My solution was to modify the BWR to 9-speed. 44-chainwheel and cogs of 12-14-16 offer a range of 327% in steps of 14-18% while weightwise still being in the ballpark of the 6-speed. For me the best compromise and I can recommend it. Cost of the modification was about 70 Euros. The 6-speed with the lower -12%-gearing would be the perfect starting point for this mod. Here is a playground to compare gear-variants: Bicycle Gear Calculator