Wait, one minute you are complaining about the current Midland Mainline TOC not taking "non-InterCity" services into account... the next you are complaining that HS2 will mean more scope to stop longer distance MML services at places like Loughborough and Bedford?
You're confounding two different problems.
Currently, there are two main stopping patterns on the MML between Leicester and London; (1) non-stop and (2) all stops to Bedford plus Luton Airport Parkway. There are variations of these, of course (most otherwise non-stop Nottingham services call at Market Harborough, some services call at Luton instead of LAP some extra stops at Kettering and Wellingborough in the peaks), but those are the main two.
Since having low passenger numbers at the "East Midland Hub" will, even if it makes some economic sense, be rather bad press for a £50bn new railway line, they'll want to do everything they can to get passengers from Derby/Nottingham to use it. The only way they can do that is by making the MML less attractive. There's no way HS2 can offer competitive overall journey times to most parts of Nottingham, Derby and surrounding areas, so the MML has to be slowed down. That almost certainly means the loss of stopping pattern (1), with all trains instead using the slower pattern (2).
In addition to that, lack of capacity at/around Sheffield will mean that far fewer services will be able to proceed north of Derby/Sheffield, breaking connections between the East Midlands and southern MML and South Yorkshire and points north.
So it's bad news for virtually everyone using the MML outside of South Yorkshire.
I'm sure the people of Leicester will retain non-stop London services and that many of them are looking forward to being able to board a southbound train without it already being full of passengers from Sheffield etc.
The only way that can work is for Leicester to become the main terminus for these non-stop London services. If they continue north then they're competing with HS2 services to the Hub. If they terminate at Leicester, that's breaking connections northwards and means the loss of the fastest London services for Loughborough, Beeston, East Midlands Parkway, etc.
Again, no good news for MML passengers.
For example, I get bored of the argument that Toton has poor connections for Derby and Nottingham because there's no shuttle service in 2017 linking the site of the HS2 station with the centres of those conurbations. There doesn't need to be yet. It'd be silly if there were! As long as there's scope to introduce that kind of thing in the future, that's what matters.
If you stopped "getting bored" and actually paid attention, the problem isn't that there is no service to/through Toton, it's that there doesn't make sense for there to be (which is, of course, why there isn't). There's nowhere logical for such a service to go; Toton is on what's effectively a Derby-avoiding freight line. There's no capacity at Derby or Nottingham for a frequent shuttle, no services (apart from a paltry few Nottingham/Derby terminators) that can be extended there and no service that can be diverted without losing stops or adding significant journey time.
The only reason that the Toton site was selected is because it's cheap; already Network Rail-owned disused railway land. There's already a "hub" for East Midlands regional services; it's called "Nottingham". This new "hub" station is not near any substantial population, not near any existing transport hubs, not on the route of any existing passenger services. It would be no better if it were not be near a railway at all!
Both the people of the East Midlands and potential HS2 users would be better off if there were no East Midlands station. Then there'd be no reason to try to force people to travel via slower routes, no need to cut existing services, faster journeys for Sheffield/Leeds HS2 passengers, no excuses for not modernising the MML (at least as far as Nottingham), etc.