My German is incredibly sloppy, but I gleaned some information from this Wikipedia article
What arguments were made to retain the Bundestag in Bonn?
Why were the two major parties (CDU and SPD) so evenly split, with the majority of SPD politicians voting to remain in Bonn?
Why was there such a North-South divide?
It bears mentioning that at this point in time, Berlin already had been declared capital of the Federal Republic of Germany with the 2+4 and Einigungsverträgen (unification contracts) and the debate surrounded the issue whether the Federal Government should move to Berlin in part or in total.
It also bears mentioning that there still are agencies and dependencies of the various ministries and others now located mainly in Berlin in Bonn, e.g. the German Foreign office still has an office building and dependency in Bonn. This ties in a lot with the very heavily federal structure of the Federal Republic of Germany, given that a lot of important state agencies (like the Supreme Court in Karlsruhe, various police agencies and so forth) are purposefully not located in Berlin in order to prevent a dictatorial take-over of all important state agencies by just taking one city.
The reason why people argued in favor of Bonn are varied but the most important ones were symbolic and economic:
On the symbolic level, Bonn had become a symbol for German democracy since 1945 while Berlin was still associated with being the capital of Nazi Germany and the seat of Hiterlism in Germany. As SPD member of parliament, Horst Ehmke, put it: "When has Germany been ever lead responsible from Berlin? Seldom or never is the answer!" At the same time, proponents of the move to Berlin argued that a move to Berlin would not only be an important symbol of new-found German unity but an explicit acknowledgement of the importance of the new former GDR federal states within the new German state.
Economically – and this explains the North-South divide and the SPD vote since the SPD is traditionally stronger in Northern Germany – it related to the presence of the Federal Government being something that brings a lot of money to a place. Bonn had expanded massively with the new government quarter throughout the division of Germany and this as well as the willingness of parliament to spend money on a place they were directly in was an important economic incentive for those MPs from Southern Germany.
In the end a sort of compromise was reached and the German government and parliament moved to Bonn over the next couple of year with the move being finished in the year 2000 but several dependencies remaining in Bonn.