The thameslink fast services are 'fast trains' so they go on the fast lines so your statement:
"swerving trains this way and that or stopping on the fast lines at all shacks"is actually wrong. I assume that your experience on TL services is limited as your "all shacks" actually boils down to:
West Hampstead Thameslink - a major interchange station
St Albans City - the busiest TL station on the MML and the second busiest station outside the zones and within 30 miles of London
Harpenden - a major commuter railhead
In fact all three of those stations have as large passenger numbers as Bedford, and much larger than Wellingborough and Kettering, so hardly 'shacks'. All of the other stations between Kentish Town and Luton have fenced-off platforms on the fast lines so no trains can stop there.
The MML operation is nothing unusual, - on most main routes away from a city there is a hierachy of train service patterns where all but the slowest all-station stoppers skip all/most of the stations on the first part of their journeys and then often turn into providers of local services. Consider:
The WCML to MK. LNW trains use the fasts and slows swapping at Ledburn & Hanslope
The GWML as far as Didcot (until TFL takes almost exclusive use of the reliefs)
The SWML (which is a SFFS configuration) has many swaps as far out as Basingstoke
The GEML has had swaps at Stratford, Ilford and Gidea Park/Harold Wood (until recently when TfL took over the Electric lines)
There are a few exceptions on some inter-city services like the WCML and ECML where cities at both ends of the journeys are large enough to have their own local hierachy of slows/semi-fasts etc..
See the Chief Planner's post above. He/(she?) has more knowledge than me of the intricacies of F-S line inter-ops. My comments are based on over 25 years of travel on Thameslink mainly off-peak but sometimes in the thick of it.
Of course anything can go wrong sometimes but the MML setup works pretty well most of the time for all. The alternative is to have a dedicated fast line to the outer reaches of the MML. It is rarely viable, let alone affordable for such an expensive project. Amazingly, there
is to be an exclusive line for fast trains to the East Midlands but it will take a few years to build, - oh by the way, it's called HS2 phase 2!