AFAIK the only differences (apart from looks and obvious things) are Cruise Control and Angel Eye projector headlamps. I would pick the Vento over the Rapid anyday
Apart from those the other differences being slightly better styling and cheaper price tag.
I was in the same dilemma last year when I was looking for C Segment Sedan, I wanted a Diesel one, so City was rejected immediately (though I love it very much). Next up the remaining cars in this segment,
Didn't want Verna as elder brother has one, Linea was rejected because it was having same engine as my previous car (Swift Diesel), Sunny did not impress the family members. Then there was Fiesta, which I was keen on due to its brilliant dynamics, features, looks. But high price & Poor sales, resale marked it down.
Then I was left with 2 choices, either Vento or Rapid. Choosing between the 2 was confusing. I chose Rapid because it was around 40-50k cheaper and I liked its styling better then Vento. Though I missed some features (Steering Mounted Controls, Bluetooth, Projector Headlamps) i felt it was a better package overall. Unlike other cities, the Skoda dealer here is very good.
So If I would choose Between Rapid & Vento, it would be Rapid if i want Diesel & Vento(TSI) if I want Petrol.