If you've ever ridden the LIRR's Port Jefferson Branch, east of Huntington, then there's a 75% chance that you've had to transfer at one of the LIRR's key intermediate stations and terminal- Huntington.
If you saw my post about capacity at Huntington, you'll know that Huntington isn't the most ideal place to serve as the terminal of the literal second busiest branch of the busiest commuter railroad in North America, but at this point, we're stuck with it.
Most of the off-peak Port Jefferson Branch "scoots" end/begin in Huntington, as the LIRR doesn't want to spend the money to send the equipment all the way to Jamaica, or more ideally, Hunterspoint Av/Long Island City. This is a common theme found on the LIRR, as on the Montauk Branch, many trains from Speonk and Patchogue end in Babylon, offload, then head back east. You also see this with the Greenport Scoot at Ronkonkoma. While many prefer the direct trains over the scoots, in many cases, all the transfer requires is a "across the platform transfer". All that involves is literally getting off the short-turn train, and in most cases, the connection is already to go, or is already arriving, then you board and after a brief wait as senior citizens and people with disabilities board, your on your way. In fact, in my opionion, I prefer this model, in most cases, over the "transfer at Jamaica" model, as at least on my home branch, at Babylon, your almost guaranteed a very speedy transfer as the electric train is typically already ready, same for the diesel in the other direction.
However, Port Jefferson Branch riders aren't afforded this same, speedy transfer as Huntington is set up a little bit different. At Huntington, you disembark from the diesel train (if your heading towards the city), then you stand on the platform while they clear the train of any stow aways (those who fell asleep by accident), before the train is given the clear to leave the platform and head towards North Side Track for storage. Following that literally seconds after the diesel clears the platform, the electric train leaves South Side Storage track to come into the station to take those passengers, before heading off on it's merry way towards Manhattan. All of this isn't speedy, and usually takes an average of 7 minutes.
The same can be said in the eastbound direction, with the electric train coming in, dumping the brakes, then is cleared of passengers before departing a couple minutes later as the diesel train enters the platform to pick up the eastbound passengers.
The LIRR Today has a video showing the move; pretty much perfectly, from a commuters POV and it pretty much sums it up perfectly.
The disadvantage to this type of transfer is it's not only more painful, but also much slower as it's typically afforded 7 minutes in the timetable, meanwhile transfers at Ronkonkoma and Montauk typically take only 4-5 minutes.
There's no real solution to this annoying transfer. It would be very expensive to reconfigure the interlocking to make it a better-transfer station, and, while it would make it faster to turn trains, it really wouldn't bring that much of a benefit beyond that, and with Port Jefferson Branch electrification to Port Jefferson likely around the corner, it's even less unlikely.
As I said in Capacity Issues at Huntington, Huntington wasn't designed as a terminal and does a very poor job at being one. However, one must give it credit for being able to terminate pretty much all the trains on the second busiest branch on the railroad, and doing so in a rather speedy manor. That's something that's pretty impressive, esspecially considering how poor it was designed.
So, until the electrification occurs, we're stuck with this setup. One that's clumsy, but I think we'll make do until they finally electrify this branch. The only solution I can think of is to extend these trains to Hicksville, where they can connect with Ronkonkoma express trains, providing faster runs and across the platform transfers. I've highlighted this in my timetable project, and the Port Jefferson Branch timetable showing how this would work will come out Friday morning.