The five-storey complex will feature a hotel, shops and a café and will be built before the V & A centre opens in the city in 2015.
Nicoll Russell’s original plans were criticised by West End Community Council for lacking character and for not being in keeping with the surrounding Victorian buildings.
But a 12-week consultation has resulted in revised plans for the £14m station.
As a result, the windows have been grouped in pairs and aligned vertically to give the building a "bolder" look.
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The orientation of the building as an east/west alignment was also in question. It was found that a north/south structure would provide better views of the Discovery, V&A and river.
A planning application for the project has now been formally lodged with Dundee City Council.
Nicoll Russell admitted in the consultation report: "A smaller number of respondents did make negative comments regarding the station building's plaza elevation. 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."
Willie Watt of Nicoll Russell said the yellow exterior also remains.
He added: "We want a range of colours that tie in with the range of colours in the centre of Dundee. 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."
(IT)
