Hm... I cannot entirely subscribe to Your view on the -400s ride qualities, as I am under the impression that it can be flown equally smoothly as any other airliner. Were the flights You described affected by adverse weather maybe, and did You sit at the rear end of the cabin? The fuselage tube is a bit prone to flexing in turbulence, and the flight attendants seated on the rear jumpseats occasionally complain about this. But let me look at the points You brought up:
There are indeed some little peculiarities to this aircraft that tend to make life less easy for its pilots. In no particular order:
Many colleagues including me find the aircraft a challenge to land. As You say, the engines move a bit of air and much of the wing is in the props slipstream, so any power change in flare will have a direct effect on sink rate. Additionally, the landing gear is very unforgiving of crabbed touchdowns; if the aircraft is only a tiny bit misaligned with the runway, it will easily result in a major impact. On top of that, an approach with Flaps 15 will normally see a pitch slightly above 0°, and to avoid the rear fuselage scraping the runway, flaring is limited to 5° nose up. This together results in a not too wide window of pitch, power setting and airspeed that has to be hit for a reasonable landing. QAR readouts in my company on the other hand show that while a normal landing may feel bumpy inside the aircraft, the G load experienced is noticeably less than on other fleets.
Just to make sure though - what I just wrote should in no way be construed as alarming or unsafe; while a normal DH8-400 landing might bruise the pilots ego a bit occasionally, it is nowhere even near to a close call and I am not aware of any -400 that was damaged due to a badly executed landing.
Another thing is the flap setting You mentioned. Flap 35° approaches come both with a remarkable nose-down pitch and a rather unpleasant airframe buffet caused by some degree of flow separation ahead of the flaps trailing edge - in rain, You will see flowing some water forward from the upper trailing edge on that flap setting. So unless performance requires such a configuration, it is generally not preferred.
Coming back to the engines. As they are way more powerful than those on the -300, they have some potential to cause an uncomfortable ride if they are handled by some ham-fisted guy. Just like in a Cessna, the prop comes with all the associated effects like P-factor, torque, gyroscopic effects etc, so any power change will require trim changes about all 3 axes; WAY more so than on the -300. If a large power change is required, it is thoroughly recommended to do it in steps (if practical, of course): move the power levers a bit, then readjust trim, then move the power levers another bit and so on; otherwise this will cause an immense yawing moment in the aircraft. While pitch trim and aileron trim changes are noticeable in the flight deck, the passenger comfort is mostly influenced by those yaws.
But just to be sure again: While this type has its weak sides (just like any other aircraft I have gotten to know until today), I find the -400 a rather agreeable aircraft to fly, with as You say remarkable performance rather comparable to a jet than a turboprop.