I know that it was fairly close after being put to a vote - I think younger people preferred Bonn and older people liked the nostalgia of Berlin, although it was a bit tainted by certain history. How did this process play out to what we have today (something like 50% of government staff in each city?).
One great disadvantage for Bonn is the fact that it is generally considered to be a city with much less history than Berlin as far as the German nation is concerned. For one thing, Berlin was the symbol of divided Germany during the Soviet occupation, and having it be the symbol of a reunited Germany held a wonderful propaganda value to show that Germany was again a nation. Furthermore, as the Prussian capital after 1701 (it was formerly Königsberg), Berlin was the centre of what became German power in 1873 upon full unification. Therefore, Berlin had a double meaning concerning a united Germany. Concerning Berlin's tainted history, though Berlin was the capital of Germany under the Third Reich, Munich was the "Capital of the Movement", the city where the Nazi Party was born and truly formed as a power party within the Weimar Republic. Many wanted to keep Bonn the capital as it had been the centre of the first successful and truly democratic German state (and these speakers were often ashamed of Prussia as well as the Third Reich) though, as the article cited below testifies, the "most passionate speakers" were those who pushed for the capital to return to Berlin. Berlin was thus chosen as the capital of reunited Germany in 1990, with the move to be completed over twelve years. The move was finished in reality in 1994 with all the power ministries moving to Berlin that year and the Bundestag reinhabiting the Reichstag Building in 1999. The vote was decided by a slim eighteen votes in favour of Berlin. The full list of agencies that moved to Berlin but kept an office in Bonn is available here (https://en.wikipedia.org/wiki/Decision_on_the_Capital_of_Germany). The article I cited above: http://articles.baltimoresun.com/1991-06-21/news/1991172061_1_bonn-to-berlin-german-capital-united-germany
The West German Constitution of 1949 (Grundgesetz) Article 22 says that the capital of Germany is Berlin, so that was it, in 1991 there was no basis for a change of the constitution in this regard (that would have been a complicated procedure).
http://www.gesetze-im-internet.de/bundesrecht/gg/gesamt.pdf
Art 22 (1) Die Hauptstadt der Bundesrepublik Deutschland ist Berlin. Die Repräsentation des Gesamtstaates in der Hauptstadt ist Aufgabe des Bundes. Das Nähere wird durch Bundesgesetz geregelt.