Out of curiousity, how are the 1310s weaker than factory? With them being recommended for small lifts and mild/moderate wheeling and 35s, I would assume they are at least equivalent in durability with the bonus of clearance being better.
You can assume that but, that's about all you can do. Factory drive shafts use rzeppa style CV joints which are really really strong. As you may or may not know, RCV front axle shafts use a similar type of joint and are all the hype because of it. Yes, the factory front shaft does have one u-joint but, it's actually slightly bigger than a 1310. The biggest reason for 1310 front shafts being recommended is because they are made with a narrower diameter tube which is needed to help prevent contact with automatic transmissions on 07-11 JK's and to help clear the exhaust cross overs on 2012's up. Also, because factory shafts use CV joints, the boots tend to sit in a constant state of pinch on a lifted JK and that causes the boots to fail prematurely. Once this happens, it's just a matter of time before the bearings inside fail as well. A 1310 shaft will not have this problem. 1310 u-joints are also very common u-joint and all these factors play a role in them being recommended - NOT durability or strength.
On the flip side if you stayed on the sub 3" lift and 35s, is it safe to say the stock front DS is the way to go over a 1310 on 2012+ JK?
On a 2012, you CANNOT run a shock that will give you more droop than would a stock JK or one that is made specifically for a 2.5" lift. Doing so will cause your front drive shaft boot to make contact with the exhaust cross over and get damaged. And, even if this weren't the case, the 2012-up JK's come with a motor and transmission that sit at a steeper angle than previous model JK's. Lifting your JK will cause the front drive shaft to sit at a much steeper angle and this will cause the CV boot to fail prematurely. These are the reasons for recommending a 1310 front drive shaft replacement, NOT added strength.