I've owned 2 2nd Gens - 2005 & 2013, which is my current truck, bought new in 2013. Neither truck has given me any issues. The 2005 was purchased used, but was without issue. I sold the 2005, then bought the 2013 by email to a dealer, drove there, signed the paperwork, never even test drove it, just drove away happy. Haven't looked back since.
When the 3rd Gens came out, I thought they were hideous. My son-in-law has one now, and it's a great truck. The looks grow on you.
I will never see any rust issues, vehicles don't rust in the southwest.
I don't think you can go wrong with either one, personally. Of course the early models of each (as with all vehicles in their first model year) had some issues, but again, you only hear about the issues, not from the people like me who have driven theirs for five years and only put in gas and oil, and rotated the tires.