Get a 2500 with air 4 link rear sus you can still get the aisen. I have a 14 with 6 spd rfe and it pulls great . My trl empty weighs 11500 k. That ex 50 lb of torque may equal about 3-5 mph up a hill. Put the the transmission$2500 or so back in your pocket. You will be amazed at how good it pulls. Goes up the same grade to my house 3 miles long 7-8 % in some places 10 mph faster and that is with 342 gears. My 06 had 430 gears. I have read about very few problems with the standard transmission.
You can't get an Aisin transmission in a 2500HD, unless I just misunderstood your post

...2500 and 3500 SRW trucks only come with 3:42 gearing, though you can get the Aisin transmission in the 3500 SRW truck, which in a 15' will give one more TQ but same amount of HP as in 13-14 3500 series.
As far as I understand it the difference between 13/14 3500 SRW to the 15' is with the Aisin you get an additional 15ftlb of TQ...didn't see any added HP, 385HP...865TQ (compared to 850TQ for the 13'-14' equipped truck with Aisin)....the 68RFE still offers 800TQ as far as I can tell be it a 13'-14' or 15'.
The 68RFE, in my opinion is a VERY good transmission, I had it in two other 3500 Dually's and never had the first issue towing my 5er, loaded to 16,200#...all towing in the mountains.
If I were the OP, I'd base my final decision on what truck to purchase by what you're planning on doing with it long term..."IF" you think you might go to a heavier 5er later down the road, I'd opt for a 3500 SRW and be ahead of the game.. If you'll stay with what you have to tow and won't be going "bigger/heavier", I'd opt for the 2500...Just have to figure out your plans "down the road".