The extra 100 tonnes over the weight used for the calculations would have some effect on the time to reach rotate speed, but I don't think it would have been that significant.
With the incorrect TOW entered into the laptop, the computed V
R is also incorrect, for starters, so the aircraft will not become airborne properly when that incorrect V
R is reached. (ie: a higher than normal body-angle is required or a tail-strike occurs during)
Since the thrust is appropriate for the wrong weight, the aircraft will not even accelerate correctly to that
incorrect V
R, let alone the correct V
R.
Incorrect V
R is reached further down the runway than computed. And in this case, even the correct V
R was not reached on the runway.
That's my point though - 'User Input' - would the pilot not increase power accordingly during the take-off when he noticed there wasn't the required power? Would an experienced pilot not have a 'feel' for a take-off (ie. sluggish performance, etc) regardless of what the instruments were saying?
The pilots DID increase power. The question is (or was) when.
In your car, you can determine normal acceleration quite easily. Engine noise and visual cues from being a foot above the ground are easy to judge. Even throttle position with your foot can help. The Airbus throttles go to the same position EVERY time (except TOGA takeoffs).
In an airliner, with eye-height that far above the ground, acceleration oftens looks insignificant. Then there's the added factor of night-time conditions which can reduce the visual cues to a series of points of light.
As for noticing the "feel", pilots are not jedi knights and The Force does not help them. Flying the same type on the same route, yes, you could reasonably expect a pilot to notice this sort of event early on.
But with the variations in conditions experienced on THREE different types of Airbus with many different weight ranges, runway lengths, airport elevations and temperature extremes, you can reasonably question whether or not the "feel" can be relied upon.
why not engage full throttle for all take-offs and adjust throttle back when safely airborne, either manually or via automated flight systems? I'll duck for cover now
If you're ducking for cover, you must have some idea what sort of suggestion you're making but you make it anyway.

I think it's been covered by now that the flex procedure is quite normal and not, in itself, a threat to safety. In the right conditions, this accident could've also happpened using rated thrust if a critical error had been made during performance calculations.