If there was a good opportunity for Barclay to appear in DS9 it was as an assistant to Louis Zimmerman.
He's established to have been involved in the creation of EMH's in Projections, a year and a half before Doctor Bashir, I presume.
Sisko kept Quark around the station because he was 'The devil you know'. He was a person with a handle on all the illegal dealings on the station, who was not a murderer and could be used to gain information on more dangerous criminals. If he had stayed in the weapons game he wouldn't have lasted on the station much longer.