For many people, the best part of a train trip is the view, now I'm not trying to say that the LIRR's view is nothing short of stellar, since if you think that you should look at Amtrak's various Long-Distance trains, but the view is still an important part of the trip, especially for infrequent riders. In the last 10 years, it's become steadily more difficult to see out of the windows on the LIRR's main fleet type, the M7. A problem that started with some minor splotching on windows years ago has gotten progressively worse to the point where your lucky to get a window where you can see out at all.
Some component in the windows make all plastic windows cloud and even yellow overtime, the M7 situation is a lot worse to the point where people are complaining. The most likely answer too this is the cleaning solution used at train washes in Babylon & Ronkonkoma yards, as these seam to have a particular effect on it.
Now while this situation isn't the end of the world; it is very annoying and could possibly bring some safety issues. Similar to why you have to put the window shade up on a plane before takeoff/landing, not just that it's cool, but because the crew needs to be able to see out of the window to make sure there's no potential issues. If you cannot clearly see out the window, the passengers and crew therefore will not be able to spot problems, and this could lead to disaster in only seconds notice. Another problem is that should god forgive need arise for everyone to evacuate, it could be very difficult for passengers and crew to judge whether or not it's safe to evacuate out of the door or window. And the problems don't end there, once emergency responders arrive on scene, it could be difficult for them to see clearly into the car, they can't determine whether or not there's someone in there in need of assistance.
Another problem with this is that on ordinary days, yeah, I'm talking about you, you peak Ronkonkoma locals, passengers might not be able to see out of the doors, therefore possibly knocking into people on the other side of the door. Also, this reason isn't that serious, but railfans who want to record out the window cannot reallt do that because of this problem.
Now, the LIRR is trying, as they have removed the "watch the gap" stickers from doors, installed on doors following a rash of gap incidents a decade back, along with one incident at Woodside that resulted in the death of a Minnesota teen. The MTA says that they can fix the issue by just replacing the windows, however, the M7 fleet is a very large fleet, the largest in the LIRR, and a big window-replacement program would have to go underway in order to replace everything. However, the LIRR already has problems with the window seals when it rains, and if you tinker with it it could cause even more problems.