Statistically, the flat junction with the highest timetable impact in the country would be Woking. It's such a capacity constraint that quite a large section of the mainline timetable out of Waterloo is written to avoid conflicting moves from the Portsmouth Direct Line.
The worst performing junction in terms of train congestion is the Selhurst Triangle complex, north of East Croydon. It's not the junction with the highest amount of delay minutes, as each train is generally delayed for a short period, however there are lots of trains, and therefore statistically is the junction complex with the highest number of trains delayed.
I don't know which junction in the country has the highest number of delay minutes, or highest delay per incident, however for a couple of years it was Acton Wells Junction. Basically, a couple of incidents where something failed across the junction, and the resulting delay to almost every freight service in London, and all the overground services, and you very quickly start racking up the delays.
Other honourable mentions are Basingstoke, which has a statistically outrageous amount of delay minutes per delay incident. This is of course compounded but the fact that almost all freight crosses the up fast, and the junction is directly adjacent to the station, making any intervention worth the cost impossible.
Newark flat junction is a timetabling and infrastructure nightmare, simply because it's very hard to ensure everything presents at the crossing at the correct time. Additionally, the maintenance cost of the junction is very high, due to the number of trains, the very high average speed, and the number of very long, heavy freights hammering the crossing into the ballast.
Heaton Norris and Slade Lane junctions together propagate delays across a wide swathe of the country. It would be a phenomenally expensive job to remodel the whole section from Stockport to Slade Lane to paired by use, however the benefits from a timetabling perspective would be highly beneficial. Statistically, this section is notorious for having both a high number of delay incidents, and a high delay per incident, and is of course compounded by completely life expired signalling infrastructure, held together with sticky tape and WD40.
Colwich is an interesting one, mainly that the junction is a capacity constraint, but the flat junction itself is a workable, if unnerving, pinch point. Grade separation would give you an extra 2 paths per hour in each direction from memory, which is neither here nor there with HS2 coming. The main benefit to grade separation would be to completely remodel the junction, and being able to stack down freights out of the way on the down slow before Colwich, and then flighting them through Shugborough. It would take a lot more than just grade separation to remove the pinch point.
Ely has been done to death, again one of those junctions that's not really an issue if everything presents on time, and therefore a junction with low numbers of delay incidents. However, the proximity of the line to Ely station, giving enough space for one freight between them, the three single lead junctions, the loop line and the yard, conspire to mean that any incidents have a very high impact.
