The winner of a stage race is the one who rides it the fastest of the pack, that's it. He can't get time bonuses "for free", as if fallen out of the sky. He should pedal for it. The only time adaptation that I can accept is the time of the peloton. When the peloton is packed, I can accept that the last of the peloton should be classified in the same time as the winner in order to prevent accidents. But that's ALL !
Time bonuses lost my favourite rider, Terpstra, a win in the Elektrotoer to Gilbert and I still can't accept it. He rode it FASTER than Gilbert and still lost because of these silly rules. It's totally unfair.
And it's also discriminatory because Niki won the prologue and the winners of ITT's are rarely credited with that time bonus. Why? Less spectacular? Maybe. But an ITT is an individual effort while in a common stage, riders can draft other riders' wheels. He deserved the time bonus more than Gilbert did for his stage win.
There are many other cases in history.
Saronni should never have won the Giro in 1983. He won because of the bonuses. Visentini rode faster than him.
Robic and Fachleitner in the Tour of France 1947. Same.
Hinault won the Dauphiné libéré in 1977 because of the bonuses (his fall should have lost him). Thévenet should have won.
In the Tour of Luxemburg 1993, Van Hooydonck was authoritative leader after his win in the ITT. Only the bonus of the last stage could make Sciandri win. And in this final sprint Eddy Bosberg was tempted to make an irregular sprint, which disqualified him from both the stage and GC (the harshest sanction ever given for this misdeed), while he was the strongest and the fastest.