I recently started playing this game again, bought the new American DLC's, I'm really enjoying myself this time around. I haven't really touched the freight routes yet but I'm enjoying the new Trenton route and the Acela. I normally do the scenarios and guided rail journeys, and I do have one complaint at the moment. It seems that the ATC and ACSES is not synced up with the speed limit or something. I don't really have a specific engine in mind for this, just anything on the Northeast Corridor I guess. I'd just like it to not switch at random moments and send the train into emergency, especially when I'm trying to make up time, it puts me behind schedule and etc. Other than that the game's better than I last remember.
Track speed and cab speed are two separate things, and they don't always align. You should always drive at the lower of the two. The HUD only shows you the upcoming track speed changes not cab speed changes and the red line on the speedometer will only ever be for track speed limits. The cab speed is displayed on the ATC/ACSES panel in cab, or in a circle to the right of the speedometer. In real life you are expected to memorize all permanent speed changes or have a route map handy with that information. You don't have to go into emergency brakes, as the beeps will stop as long as acknowledge the warning and put your brakes into suppression. You can release the brakes when you are at or below the cab speed displayed on the ATC/ACSES device in-cab and carry on.
When they are synced sometimes the cab speed will suddenly drop and I don't have enough time to slow the train down before ATC kicks in and it's hard trying to press the button fast enough using a controller.
You will get to remember those areas and respond sooner as you learn the route because I agree it's quite stressful when you hit one of those areas unexpectedly. Also remember that signals will affect your cab speed, so if you're against an adverse signal it may decrease your cab speed as well. There is a very comprehensive guide to the systems put out by one of the main authors of Boston-Providence, I think it's very interesting and informing. Although this is for Boston, a lot will apply to New York-Trenton as well.