Which will offer better future water cooling options (Custom and/or AIO)

The Fractal Define S has more cooling options than the Pro M , it supports up a 420MM rad up top and a 360MM up front, with the Pro M you can only use a 360 and maybe a 120MM provide you want to use some 3.5 HDD' so the Define S would win here.

build quality

The Fractal Define S side panels are solid, I would even be willing to say you could use one for a weapon, I accidentally dropped mine on the foam that came with the case and it sliced though it like butter and its heavy but the case it self isn't super sturdy without the panels but with it on it is. The Pro M has flimsy side panels but a solid actual case so I would say they are even here.

build quality

I would also say they are even here too

be easier to build in

I would have to give that to the Pro M for having a basement which makes cable management easy, in the Define S things can get tight but its doable.

OP, I'm finding myself facing the same decision. What did you end up doing?

I think I like the pro m better today, but the define S seems like the better long-term solution.