Personally, I never had a problem with subways. In fact, I think they're awesome! Especially games like STTNG, TAF and MET where it adds to the theme of the game.

-In TNG, the balls are "teleporting" from another area, along with the beam sound during return for effect. Really cool.

-In MET, the ball appears to get smashed underground by the hammer, then rolling into the coffin lock through the transparent window. That, along with the badass animations make it fit like a glove.

-In TAF, the ball disappears behind the rotating book case, then returns the ball via the swamp scoop. It adds to the fun mystique of the mansion in the film, with all the nooks, crannies and secret passageways. Enter in one hole, emerge somewhere else!

There was always a visual and audio cue (flashlamp and sound effect) to let me know where the ball was coming from without any nasty surprises. I'd love to see more subways utilized, as long as it fits the theme.