The original plan was criticised by West End Community Council, who said it lacked character and was out of keeping with the Victorian buildings round about.
Architects Nicoll Russell of Broughty Ferry carried out a 12-week consultation at which they received many comments from the public — most of them supportive.
Now, the windows of the crescent-shaped structure — previously likened to a ''banana split'' — have been grouped in pairs and aligned vertically to give the building a ''bolder'' look.
A planning application for the project has now been formally lodged with the city council and is likely to be considered next year.
The five-storey complex, over an archway and featuring ticketing facilities, a hotel, shops and cafe, is to be built before the V&A opens in 2015.
''A smaller number of respondents did make negative comments regarding the station building's plaza elevation,'' the architects admitted in their consultation report.
''The project team have chosen to take these comments on board and therefore to enhance this elevation.
''We believe we have struck a balance which addresses their comments while maintaining the general appearance of the building, which other respondents supported.''
They added: ''We therefore believe the public consultation process has contributed successfully to the revised design of the proposals, which now form the basis of the planning application.''
West End Community Council chairman Andrew McBride likened the original plan unflatteringly to a banana split and questioned the east/west orientation of the building.
He believed a north/south structure would provide a better welcome for visitors in offering views of the Discovery, V&A and river.
The orientation of the design has remained the same, however.
Other factors to do with the building's relationship with the station square, the archway entrance and the station platform and railway track supported the case to keep the east/west orientation.
The yellow exterior also remains, as Willie Watt of Nicoll Russell explained.
''We want a range of colours that tie in with the range of colours in the centre of Dundee,'' he said.
''These range from tanned and bronzed colours to some that are quite dark and melancholy. We have deliberately chosen a colour at the lighter and more cheerful end of that spectrum for the station exterior.''
The £14 million cost will come from Dundee City Council (£8.6 million), a European Regional Development Grant (£2 million) and the Scottish Government (£1 million).
Discussions are taking place with Network Rail for the remainder.