Southern were going downhill long before the merger with Thameslink.
Crew diagramming was getting tighter and more complex.
Stock diagramming was the same, the suburban and mainline were getting more interwoven, coupled with the use of more complicated formations.
This also affected the maintenance regime too.
The timetable was designed for no incidents! As soon as one occurred, then late running started to build up due to the nature of the stopping patterns with the service.
In the meantime Thameslink was subject to all sorts of problems, of which only some were of its own making!
Since the join up of the two, diagramming has got tighter on Thameslink too, with less spare capacity to recover.
However, probably the biggest offender of causing delays is the state of the infrastructure on the Sussex area, with failures somewhere every day. Hardly a day goes by without some track or signal failure on the Brighton mainline, and with the level of service provided, disruption soon follows, requiring a reduction in the service too (as per the Service Recovery Framework 'agreed' between the TOCs and NR).
Once the service starts to fall apart, the only way of often recovering is to 'slash and burn', especially the more outer extremities of the network.
However, it could be argued too that this is a result of trying to win a franchise at all costs, and reduce overheads, be it crew, stock, maintenance etc.
