The first one comes down to will. I was born less than a decade after the stretch between Hicksville and Ronkonkoma was electrified, and east of Farmingdale, this stretch was merely single-tracked with sidings. The latter project was only somewhat cheaper than the last estimate for electrifying the rest of the Port Jefferson Branch, but finishing PJ electrification has never been considered a high priority, hence the lack of investment for the last 40+ years. Oyster Bay also has a short electrified portion and that's it, yet it's almost entirely double-tracked, which is insane when trains almost never run more frequently than every 120 minutes.
The third is hardly surprising when you lack the ability and/or will to provide even remotely better service, which is a common issue with diesel service, as they have (at best) mediocre C3 availability and laughably poor locomotive availability, hence the lack of service east of Ronkonkoma and along the aforementioned Oyster Bay Branch (which is further influenced by the flat junction in Mineola). This and the above create a negative feedback loop that could be addressed with greater electrification and a fleet expansion, among other things.
The second one is absolute bullshit. Diesels emit far more particulates than electric trains and require a far more finite power source with inherently terrible efficiency (internal combustion produces plenty of waste heat in addition to those aforementioned particulates).