I had '98 Tacoma (4cylinder, 5speed manual Extended Cab) that I sold off a while ago. When I wanted to get another 'small' truck it was toss up between 1 gen behind current Tacoma or the D40 Frontier... but wanted V6 and 6 speed manual. Then having experience with my Dad's newer Tacoma and not really liking it as much as my previous 1st gen Tacoma decided Tacoma was out of the running. D40 Frontier it was... better driving position and chassis, more torque than the Tacomas, fully-boxed frame, utilitrack system, a better truck looks to me. Found 1 of only 2 in the country at the time which met my requirements (4.0L V6, 6spd manual, 2WD, and King Cab) and did a fly'n'drive and had a nice trip bringing it home from North Carolina.... Raleigh to Houston. '13 SV with 81k miles on it when I bought it.
I've now had it for just over 3 years and won't even think of getting rid of it, like it much better than my previous 1st gen Tacoma... 1st of all never going back to anemic 4 cylinder trucks after experiencing the 4.0L VQ... will flat out spank my FR-S to 80mph... pulls like a freight train to ~90mph where aerodynamics start taking over and slowing things down. The size and weight just seems about right, wouldn't want it any larger or heavier.
Stock suspension was a little tired feeling... have refreshed suspension with a full OME (Old Man Emu) offroad suspension kit to get a little bit better clearance and man what a difference in ride quality, much more buttoned down and quicker to change direction while being lifted around 2.5". Ride very much reminds me of my FR-S... very taught and direct feeling but soaks up bumps well. I even did a little 'Prerunning' on some desert trails with it to test it out and man... at ~90 mph on primative gravel, light silt, and slightly wash-boarded surface it was almost as good a ride as cruising on the highway.... and took some air with about a foot or two jump at 65 just past a cattle-guard with ease. The Kumho Crugen HT51 tires I run not only are excellent highway cruising tires but do EXTREMELY well on loose dirt/gravel/light silt... Cannot recommend those tires enough... simply awesome tires!
The main weaknesses it has stock are it's brakes and headlights... and seat. The brakes always felt just not quite good enough, which was fixed via switching to Hawk LTS pads and new Centric rotors. The poorer than average visibility with factory lighting (which FR-S also shares) was fixed via a Diode Dynamics HID conversion kit. With the HIDs, cruising at 90mph on Interstate at night you can clearly see 3 seconds or road ahead, with highbeams on nearly 6 seconds of road (not counting reflectors on the side of the road... which clearly light up over 1/2 mile away, some 22-26 seconds.) Am looking to go with a nice projector beam conversion after experiencing updated lighting on my FR-S via LED bulbs in the stock projector housing... much superior to HID setup with reflector headlights...just freaking expensive. I actually just installed new fog lights on my Frontier this evening, as a recent trip back from Austin about a month ago resulted in my drivers side fog light being hit and shattered by something. The new lights (Diode Dynamic SS3 Sport) are MASSIVE improvement... very tight and narrow in height with WIDE throw... talking absolutely lighting up things 50+ feet directly to either side in an 80 degree spread with the SS3 fog light housing/optics.
The factory seat in my Frontier is as good as my factory Tacoma seat was... which is to say it's pretty bad for comfort. Any trip over 20-30 minutes starts hurting. Most all stock vehicles seats suck for comfort for me, which is why they eventually get replaced with something I know works for my body. I've yet to replace the Frontier seat, but have it's replacement ready to go - just need to fabricate mounting bracket for it.
Have not had any issues with my Frontier other than having a complete failure of the brake system about a year ago. Think it was just the master cylinder that went out... had this happen before on another used car I bought (Acura Integra). Thankfully with a manual transmission you can efficiently engine brake to a stop. Went ahead and had dealership 'take care' of it since there was a recall/service bulletin for SRS system recalibration to prevent accidental discharge under certain circumstances (related to high pitch angles and rough terrain) I wanted them to do. Dealership had their one chance and seriously blew it... that Nissan Dealership will never get my business again for anything. It took several months to source the ABS actuator they claimed it needed after they checked over the brake system and told me the master cylinder was fine (I told them pretty much thought it was the master cylinder gone out), destroyed my nearly brand new Hawker Odyssey battery from negligence (ran it down to 3 volts...), had the gall to say I had a bad battery and needed to buy one from them, and once they got the ABS actuator installed... what do you know... they had to replace the Master cylinder as well since braking wasn't what it should be.
So other than the dealership, the experience with my Frontier has been pretty good and I wouldn't trade it for any Tacoma.