When in auto mode ("D" mode), the computer doesn't downshift until the rpm's go down to 1500 (or unless the throttle is pressed to the floor). That is not much above idle. It can be in 5th gear at about 2000 rpm and climbing a hill and if the throttle isn't pushed to the point at which a downshift is forced then it will remain in 5th and be lugging or on the verge of lugging. Inability to accelerate without downshifting and engine vibration and noise are the symptoms. This is damaging to big end bearings exposing them to low oil flow and pressure while placing them under heavy load when the crankshaft is rotating slowly. The bearing material gradually wears, bearing clearance increases, oil pressure is reduced, bearings may seize and connecting rods may break, and the rate of damage increases until the engine requires a major overhaul - in the case of this engine that probably means a replacement and that will be when the engine is no longer warranteed.
This engine has very little torque at rpm's below 2500, and certainly below 2000 which is the level at which the shifts take place in "D" mode for most driving situations in urban conditions. Using wider throttle openings can force it to shift at higher revs but it won't maintain a specific gear when that is required since it's programmed to keep shifting upwards regardless.
Higher engine speeds reduce the liklihood of big end bearing damage from load induced knock.
There are some misunderstandings caused by the confusing programming of this transmission and by lack of knowledge and maybe experience. You cannot accelerate faster using the manual mode. In fact, it will accelerate faster in the auto mode, practically speaking, because all you need to do is to keep the throttle to the floor and it will shift at redline. That is difficult to time well in the manual mode. Also, the time it takes for each shift is exactly the same for the manual mode as it is for the auto mode since the computer is in control of declutching and reclutching, and it takes its sweet old time doing that too.
Unfortunately it is also not practical to drive the car by keeping the throttle pinned to the floor. When you don't do that, and that is virtually all the time, the computer is programmed to shift at as low an rpm as possible and to continue to shift up until it reaches 5th gear regardless of the suitability of doing so. This is to get the car into the highest gear at the lowest rpm and the widest throttle opening which is the way to achieve highest fuel mileage. Trying to defeat this programming by using wider throttle openings while accelerating only frustrates.
The programming is more suitable for the diesel engine, but not for this small gas engine. The engineers may not have gotten it right - the requirement was to program the transmission in response to a marketing priority, not drivability or engine longevity priorities. This is actually abusive to the engine.
It's possible in the coming years that these cars, driven particularly in the auto mode, could begin to exhibit bearing problems - and I hope this post will be remembered then. The only thing that may be saving matters for now is the use of high quality synthetic lubricants. That may not be enough, however. Driving in auto mode and trusting that the engineers got it right is putting your faith in something that is not defensible from a technical viewpoint. If a mechanical knock becomes noticable especially at idle when the engine is warm then the problem is beginning.
Here is some information on engine noises -
Engine Noise
And rod knock -
Rod Knock
To recap - to get best performance use "D" mode - to get best fuel mileage use "D" mode - to get best drivability use manual mode - to get smoothest shifting use manual mode (with effective throttle manipulation) - to keep the transmission in a suitable gear for any situation use manual mode, to assure that the engine will not be lugging use manual mode.
There might also be a misunderstanding of how the shifting is designed - it is a sequential shift, not a gate shift, and that is a good thing. Trying to change it to a gate shifter would only make the situation worse. There's nothing wrong with sequential shifting - to downshift you tap the lever or paddle any number of times required to reach the gear desired. Reverse that for upshifting. That is actually easier and faster than having to locate a shift lever into a specific gate. To get neutral all that's required is to shift the gear lever up one position to "N", and that's as easy as with any gate shifter.
To shift manually you really do need a tachometer to know what rpm the engine is operating for both up and down shifting. There is a sweet spot for effective up shifting and that is in the range of between 3000-4500 rpm. Depending on the situation you can go a little lower or higher. For downshifting you need to know what the rpm will be after the downshift so as to not over-rev or lug the engine. Keeping the rev range between 2500 to 5000 is the area that is safe and practical to use.
One other thought to mention - don't shift to 5th gear unless the road speed is at least 50 mph (80 kph) or higher. (BTW - the car will reach maximum speed in 4th gear).