Yes please. This was one of my favorite things about Spirit Tracks. The teamwork puzzles in the Tower of Spirits are among my favorites in the series. I want more like them.
I've always loved having a companion along. Adventures are more fun with more people. I've been saying for a while that I want companions that act as party members and help you fight. I want to see something like that.
Companions definitely shouldn't be scrapped. They tend to be very helpful...