I would Pick the BIG one.
If you plan on keeping the machine, whenever you go to sell it the 128GB drive will be failing from favor much faster than a 256GB.
In 3 years the 256GB will be like the 64GB is now.
The resale value won't be much higher. You would be lucky to recoup the premium you pay. It makes no sense to spend $2 just to gain an extra $1 later.
Example: on eBay right now (looking at Buy It Now only) you can find original 16GB iPads for around $350, with one unit around $330.
So that means 32GB ones sell for $450 right? Nope. 32GB ones are around $375-$380 (with shipping), with one or two units at $360.
So basically, those people paid a $100 premium but that is resulting in just $20-$30 in added resale value on average.
If those people bought it only to maximize resale value, they would have been better off keeping the $100.
$499 iPad resold for $350 = $149 loss
$599 iPad resold for $380 = $219 loss
My point is that making a decision to get upgrades if you don't need them just to "maximize resale value" is a financially losing proposition. Only get the upgrades if YOU need them.
And in two or three years time if you decide to KEEP the machine longer but need more space, you can always use the money you saved toward an even better/bigger/faster SSD for your MBA.
And let's be real here, if you are a techie, holding onto one computer for over 3 years is not a position you want to be in unless money is real tight.
With the 13" you can also get SD cards, so if you get really desperate for more space you can get SD cards for media for less money (especially in a year or two as SD card prices go down).