What about adding the possibility of byo-yomi periods in the time settings?
When I play against a player with 1000 running games, he or she mostly moves the last hour before time-out. So I have to wait 7 days for each move to be done. "Well, set the time limit on 2 days", but sometimes I want to think longer about a difficult move.
When you add the possibility of byo-yomi periods the players can time-out a fixed amount of times. F.i. when two players use one day per move and they use 5 byo-yomi periods, each player can time-out 5 times a game. When they time-out a new period of one day starts.
This system is used in the game of go.