Here's another idea:
Ranged- attack ground units that, for the purpose of balancing, can only attack enemies at a set distance, no more and no less. Their range will be longer than towers of the same level, and so they're superior to towers. But since they can only attack at that range (and no less), they will not be able to attack the usual fighter units when at melee range. Also their missiles always fire towards the original location of their target at the time of firing, and will not damage the target if it has moved from that location, so basically it can't hit a usual fighter unit.
To balance this out, towers should be made much more damaging than they are now, or let melee fighters have lower hit points, so that towers are superior to melee fighters, melee fighters are superior to siege weapons, and siege weapons are superior to towers.
They can't hit explorers because they're ground-based, and explorers can't hit them because they're not organic units. They can be manufactured at a new type of building (factory?) using wood + stone carried in by workers, and they're upgraded by upgrading the factory. Higher level will mean more resources needed to build each one.
Please criticise as appropriate :)