Because its saves money in procurement, maintenence and training. For example a metaphor might be in schools, they have black boards and white boards. One requires a supply of chalk and to be chemically cleaned every couple of years, the other requires a supply of pens and a different type of cleaning process. The school would save money if it standardised and only had to buy chalk or only had to buy pens rather than being forced to keep a supply of both.
There is also the question about areas where the employment of overhead wiring is impractical, for instance the Watford DC lines, the Northern City Line and I imagine parts of Merseyrail.
If you do not replace these areas you loose many of the benefits of conversion with regards to parts standardisation as you would have to maintain seperate stocks of parts for these areas anyway.
The lines would only be hybrid for a year or two allowing stock to be cycled, theres an abundance of dual voltage rolling stock in the south.
You seem to be assuming you can somehow obtain the elimination of the third rail supply within a "year or two", in order to avoid the nightmare that would be a dual signalling Clapham Junction it is likely you would have to convert the main lines out of Victoria and Waterloo simultaneously, which accounts for the bulk of the traffic on the Southern Region I would imagine.
Having main line trains switch power on busy main line routes in the South would be potentially disasterous as a train that suffers a failure of switchover could cause massive delays, which means the switchover and resignalling would have to be done in a single massive campaign, especially as any switchover points would be expensively dual signalled even if was only the break between the systems for a few days.
Then there is the hardening to the South Easts power supply that would be required to cope with the massive unbalanced traction loads required by an AC supply system as compared to a 750V system that can draw from all three utility phases equally.
Oh andt he fact that all the electrification staff in the Southern Region and merseyrail would have to be massively retrained to deal with the new system with the attendant difficulties.
This conversion would have to be done at once or not at all to avoid all sorts of horrific expenses associated with partial conversion.
In the end Im not convinced by the business case as compared to spending the capital in other areas with greater benefits (such as the MML).
Additionally the entire electrification system is unlikely to be wearing out at once, so you would have to scrap parts of it ahead of others and have temporary switchover points rather than simply doing it all at once unless you want to scrap vast areas early and thus write off the remaining life of the system with all the attendant increases in track access charges.
In most countries there are multiple overhead voltages (15kv, 25kv, 1500v DC, 3000v DC, 750v DC) rather than differing transmission systems, these countries are also standardising and phasing out the less common electrification systems like 15kv and 1500v so that trains can operate across Europe more freely.
I was also referring to the New York area where they have at alast count, 5 transmission systems in operation: 25kV 60Hz, 12kV 25Hz, 750V top contact, 750V bottom contact and 600V top contact.
The 3rd rail system also precludes trains on the lines in future operating at 110 or 125mph speeds.
As has been stated above, there are very few areas where running at 110mph or 125mph would be practical due to the close station spacings and the high stop frequency of most services, additionally running trains at 125mph instead of 100mph would erase your 20% total energy saving due to increased air resistance.
