1) You don't keep a deep coal mine clear of water without pumps. Pumps which use power presumably, unless perhaps they can be powered by geo-thermal energy?
2) Bringing massive amounts of highly polluted waste water to the surface. Where does that go? Getting the water out is not a one-time operation, but would presumably need a big decontamination plant to handle keeping them dry long-term. Don't the Council remember what was chucked down the mineshafts when Shelton Bar and the other highly polluted industrial sites in the city were cleared and decontaminated? All that sludgy water down there is not likely to be very nice. Dealing with it in huge open evaporation ponds might not do a lot for the new green eco-friendly image that the city is currently crafting.
3) Some of the recreational lakes in Stoke could be drained dry by draining the mines, because lakes such as Westport Lake apparently let down into 'bottomless' flooded coal shafts. Or so I was once told by an old local Councillor who knew the area well as man and boy.
4) The possibility that draining the mines could cause mine collapses and thus housing subsidence right across the city. There used to be fairly frequent housing subsidence due to the mines but that stabilized around about 2003-ish and has hardly bothered us since (despite what the Council's spurious housing-clearance surveys have claimed). I really wouldn't want to risk triggering housing subsidence again, if I was in the Council and keen on being re-elected. And what is being planned is directly under the city, as the council themselves said in a report for the Green Bank, the city is...
"the only English city immediately above sources of geothermal energy and coalbed methane reserves"
Maybe it can work. It's been done elsewhere, although seemingly not directly underneath a major city. But all in all, I reckon environmentally responsible shale gas extraction would be a far better option to explore, in terms of bringing much-needed cheap power to the pottery industry safely and cheaply.