Although I'm hardly a big writer, some suggestions:

-Read up on the Hero's Journey: http://en.wikipedia.org/wiki/Monomyth
-Combine 2 stories. Alternate chapters between one and the other
character(s). This is a great way to add small cliffhangers aswell midstory.
Once in a while have them meet eachother and use common places, elements and
people in both stories.
-Add multiple points of view: Not just main hero fighting the big bad, but
for instance also the bid bad's closest advisor. This will make the penultimate
chapter where your 2 main protagonists meet very interesting.
-Don't be afraid of using anti-heroes; personally I find Batman more interesting than Superman, Lara Croft more interesting than Link from Zelda.

Just my 2 cents,
Greever