It's funny how this old chestnut keeps cropping up time and time again 
IMHO, the Thameslink tunnels were a prototype to see if RER-style services worked in London. Experiment successful, they do, and thus we have Crossrail under construction.
As people keep mentioning but without nailing it down, you can't sensibly mix stopping patterns in a high-capacity railway. There's a reason the 'New' DC lines were built on the WCML...
Now we've established Thameslink works, lets do it properly. A new bored tunnel from West Hampstead to somewhere suitable, perhaps East Croydon, perhaps just Herne Hill, and extended 6-tracking out to the limits of the metro service. Regardless, the existing slow Victorian route can then be used for what it was designed to be used for - slow Victorian-esque all stations services, aka the Thameslink metro services. Give the new TL tunnel just major station interchanges to keep it nippy, and jobs a good 'un. Thameslink can then operate as the comfortable 100mph suburban railway it needs to be to serve Bedford/Cambridge/Brighton, and the metro services can have suitable high-density stock running all stations up to 75mph.
In the context of Crossrail, London is a lot wider than it is high, so there are always going to be more stations across it, so mixing the two is more acceptable. Really, there needs to be 6 tracks out to airport junction, and Crossrail can then operate to Slough/Heathrow/High Wycombe all stations with the same 75mph metro stock as Thameslink out to Shenfield and Dartford. On the relief/slow lines you can then operate the faster-geared suburban stock (with toilets!) out beyond there to Reading/Newbury/Didcott/Bicester/Oxford and Ipswich/Gravesend etc.

IMHO, the Thameslink tunnels were a prototype to see if RER-style services worked in London. Experiment successful, they do, and thus we have Crossrail under construction.
As people keep mentioning but without nailing it down, you can't sensibly mix stopping patterns in a high-capacity railway. There's a reason the 'New' DC lines were built on the WCML...
Now we've established Thameslink works, lets do it properly. A new bored tunnel from West Hampstead to somewhere suitable, perhaps East Croydon, perhaps just Herne Hill, and extended 6-tracking out to the limits of the metro service. Regardless, the existing slow Victorian route can then be used for what it was designed to be used for - slow Victorian-esque all stations services, aka the Thameslink metro services. Give the new TL tunnel just major station interchanges to keep it nippy, and jobs a good 'un. Thameslink can then operate as the comfortable 100mph suburban railway it needs to be to serve Bedford/Cambridge/Brighton, and the metro services can have suitable high-density stock running all stations up to 75mph.
In the context of Crossrail, London is a lot wider than it is high, so there are always going to be more stations across it, so mixing the two is more acceptable. Really, there needs to be 6 tracks out to airport junction, and Crossrail can then operate to Slough/Heathrow/High Wycombe all stations with the same 75mph metro stock as Thameslink out to Shenfield and Dartford. On the relief/slow lines you can then operate the faster-geared suburban stock (with toilets!) out beyond there to Reading/Newbury/Didcott/Bicester/Oxford and Ipswich/Gravesend etc.