Covid has made a mess of things but LIRR, for planning purposes, will assume that things will eventually get back to 'normal'. However, smart companies will review how remote work is in real life, how expensive Manhattan is, yet understand that requiring employees to either commute huge distances or resign doesn't work. Instead of constantly expanding space in Manhattan or creating places too far from Manhattan for many people to reach, it's better to have mostly remote work for certain jobs, 'hotel' desks shared my many centrally, and train people and managers to effectively work and manage remotely. Some firms will understand that this can be a win-win for both the firms and employees, and for the environment. So long term there will likely be fewer long distance commuters - unless, of course, MTA & NJT finally understand that they need good, effective interconnects between regions. But it's pretty clear that none of the regional transport agencies get this. But making rail lines work better will still be needed. Outer lying areas like the PJ line and east of Ronkonkoma and Oyster Bay, etc., still need double tracking and electrification. But if they ever get it right, it's unlikely to be in my lifetime. They are just too incompetent and corrupt.
At Jamaica, it will be extremely difficult to ensure that easy transfers are possible. And given that too many planners still think that diesel country doesn't deserve decent service, it's highly unlikely that they will ever get it, including reasonably decent connections at Jamaica. Even that the LIRR president lives on the PJ line (Smithtown?) doesn't seem to make any difference.