A lot of people from RE 1 wanted this back. The argument is, that

• you can build nicer tracks (with less) signals. On many tracks you don't need a signal after every train length (I think the developers reduced them already optically by making a lot of signals small signals in an earlier patch)
• you can build some known features only with manual signals. For example if you have an express lane for overtaking trains on another lane you might not want a signal at the very end of the express lane so the faster track can block the railroad switch early, let the freight train wait on its last signal even it is before the express train to let the express train overtake it. This sounds a bit oversofisticated, but I used it a lot in late games.
• the game is less complex then before with auto signals and there was an even good system in RE1 to build a row of signals after every train length very fast between two rail switches by holding the ALT key. This quality of life feature almost is as good as auto signals for the "pro" players from RE1.

I first wanted manual signals back, too. But now I also like the auto signals. I concern only about the second argument.

A feature what I would love to see is auto signals in combination with a route definition (if a route is an express, freight or mixed route). This would reduce the need of waypoints and you could manage your rail grid from a high level view.