MHO, 28s really aren't well suited to lots of rail trails if they aren't paved. You want at least 32s or 35s. Also, don't be afraid of mixing sizes, with a 35 on the front and a 40-45 on the rear. Mixing sizes can give you very surprising results. You can have comfort and handling!

My experience with Borough tires is that they were like riding on lead. Not so with other Specialized tires. I love Schwalbe Marathon Supremes, but maybe not best suited to that type of riding. The "tread pattern" of the other Marathons should be sufficient, and a good alternative.

There are also a number of minimally treaded tires which will be fine, just try to stay away from slick type tires. The rail trails you describe want some type of tread for traction, but it doesn't have to be knobbies.