In regards to services on the ECML and MML after HS2 phase 2 has opened, you have to remember that between then and now there are plans to increase capacity on those routes, and that the cities of Peterborough and Leicester will still warrant fast services from London.
For the ECML Network Rail wants to upgrade the line to support 8 long distance tph (West Yorkshire, North East & Scotland).
South of Peterborough the ECML will see an increase in capacity with the start of Thameslink services in 2018. In the peak this will see, 4tph to Peterborough (2 from Kings Cross & 2 from Thameslink), 6tph to Cambridge (2 non-stop from Kings Cross, 4 from Thameslink, 2 fast & 2 semi-fast), 6tph to Welwyn Garden City (2 from Moorgate, 2 from Kings Cross & 2 from Thameslink), 8tph to Gordon Hill/Hertford North (all from Moorgate) and 2tph to Stevenage via Hertford North (from Moorgate).
In terms of what could change on the ECML after HS2 phase 2 opens in my opinion would be more calls in the Long Distance services added for Peterborough (were potential all service could call), Grantham, Nerwark North Gate, and (1-2 tph at) Retford. The only station south of Peterborough being served being Stevenage, so that the majority of services from Peterborough run non-stop.
A similar situation applies to the MML, where Network Rail is investigating bring back 4 tracks from London to Kettering in addition to electrification will increase capacity north of Bedford to support 6tph from the MML St Pancras platforms (2 semi-fast tph and 4 fast tph south of Leicester). As well as this from 2018 Thameslink will see 16tph in the peak south of Bedford.
As with Peterborough, Leicester will still warrant fast services to London after HS2 phase 2 has opened. In my opinion the most likely outcome would be either, one call added to each of the 4 long distance services south of Leicester (1 calling at Market Harborough (as now), 1 at Kettering, 1 at Wellingborough, & 1 at Bedford), or 2 trains continuing to run non-stop from Leicester and 2 calling at additional stations south of Leicester out of the 4 long distance services.
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I accept your reasoning about slower services, but if you live in, say Grantham or even Peterborough (or on EC, anywhere south of York really) and already commute into London, how will you feel about having to take a much slower service without any viable high speed option? I would suggest that if all EC, MML and WC services are inhibited by more stops or just slower timings, this will be a deliberate move to push people onto HS2, in the same way that many Kent services were slowed after the Javelins were introduced. I can't see this going down too well.
This is where things get confusing with the ECML. As slowing down could mean anything from more calls south of Peterborough, or not running non-stop from York to London. I would assume the latter, as HS2 services will effectively replace the current non-stop and fast services from York to London, and would allow calls at places like Peterborough and Grantham to be added.
You could have a calling patter between Doncaster and Kings Cross with 8tph like this:
2tph Doncaster-Peterborough-Kings Cross
2tph Doncaster-Newark North Gate-Peterborough-Kings Cross
2tph Doncaster-Grantham-Peterborugh-Kings Cross
2tph Doncaster-Retford-Newark North Gate-Grantham-Peterborough-Stevenage-Kings Cross