Rough, smokey idle and MPG drop are the most common.
improper filtration is another one...
to the original poster.. id check DTCS as well before buying it...
I have 230K on mine, stock engine, other than a smarty on level 5, it needed injectors at 200K on the dot... and what happened with mine was sticking injectors, and raw diesel out the tailpipe, you would throttle a bit and it would stick.. anyways with 230K on it, I tow with it weekly, loads from 5K to 15K or so, I tow my horses and gooseneck, (roughly 10K) once a week it has a stock transmission, it does ok with yearly fluid changes, only have had to put the solenoids in it once, I do the fluids and band adjustment once a year on it, It also starts up really quick most times (once every two weeks it cranks over one extra turn or so, I assume it an injector returning too much fuel), it does not make any oil, does not need anymore oil (above the safe line) every 5K miles when I change oil and filters, and I have NO BLOWBY.. by blowby I do not mean the steam coming out of the crankcase tube below the truck, I mean crankcase pressure that will blow the loose cap off of the oil cap. Simply said, take the oil cap off on a warm engine, (up to temperature) and loose just like it came off, put it back on the oil fill hole, if there is pressure in the crankcase (enough to blow it off of the oil fill hole) then you have serious problems, ranging from a broken ring, or bad piston...or worse... if you put the cap on there, and it just dances around so to say with the vibration of the engine, alls well for the time being..... (knock on wood for mine).. anyways, mine has steam coming out of the tube, and very little from the oil fill hole on a warm engine with the oil cap removed... but it does not blow off the cap like a volcano, cap just dances there when It is put on loose as I stated above........ Like any other truck, they have issues, with mine is been mainly electrical demons, usually stemming from codes for the fan clutch (PO483) or some grounds or other connections loose... front ends, as stated, are crap on these trucks, done mine already twice in five years of ownership
also, if its making oil, its time for an injector or more.. one or more bodies is cracked at that time..
overall they are a much nicer ride, make smoother power, and more creature comforts than a second gen, but it comes with a tradeoff of different demons than what you are used to for the 12 valve... also.. IIRC, an overhaul for a commonrail cummins is recommended at 350K miles or so, and the lifespan of injectors is right at 100K or so with factory filtration (five micron) but you buy some more time with two micron filtration, which is what is required as per bosch standards...
oh and yes, the kit from Glacier Diesel performance is AWESOME.. I run that for a two micron filter