I have owned my Dakota for 9 years, bought it used with 42,000 miles from Carmax, I myself have now put over 132,000 miles on it since then. Without even a shred of doubt it has been absolutely the very best vehicle I have ever owned. There may be "common issues" with Dakota's but none any worse or better than any other truck out there.
Yes the 3.9 is not exactly the fastest on the street. Mine runs perfectly fine for me. I keep it tuned up and in good shape. I had one HVAC actuator replaced under the Carmax warranty right after purchase. The blower motor resistor does tend to burn out, it helps to replace the resistor and the blower motor both at the same time. Usually when the resistor goes bad it is because the OEM blower fan is drawing too much current. I guess you could call both of those common problems. If a blend door actuator fails the HVAC will default to defrost mode.
The ball joint problem was covered under recall, but only for upper ball joints on 4 wheel drive Dakota's. I replaced all 4 of my OEM ball joints around 125,000 miles so I will say I got my money's worth from them. Dodge says to replace the control arm as an assembly, but on 2 wheel drives you can drill out the rivets and bolt in new parts. 4 wheel drives have riveted upper and pressed in lower ball joints which can also be replaced fairly easily.
I heard or read somewhere that Dodge was said to have fixed the belly pan gasket problem some time in the 2000 model year. Some trucks have the problem, some do not, but Hughes Engines makes a great kit to replace the gasket and pan permanently.
I have never had any water on my passenger floor, and I use my A/C a lot, living here in sunny Florida. There is an elbow you can get from Dodge to put over the A/C drain if you have the condensate blowing back in at highway speeds.
I can't speak for any rust, we don't really have that problem here. I have the NV3500 manual transmission, it has done a fine job, is very strong but my throwout bearing is a little noisy. From what I have read, they all are and it does not bother me.
My Dakota has been great. It has never let me down and never left me walking. It runs and drives great for its age, it handles well, is super comfortable to drive, the interior is still in near perfect shape even at over 13 years old and my truck is pretty easy to work on. I track my MPG on
www.fuelly.com and routinely get right at 18.5 MPG in mixed city/highway driving. The parts I have replaced and repaired were all either normal maintenance items like tires, shocks and brakes or parts that failed due to high mileage, which is to be expected. My only regret is I can not go back in time and buy my Dakota brand new.