I am picking this up because of a recent game i played.
playing ptolemies against seleucids or carthage (not sure anymore, he had ele's and chariots) i an multiplayer game on a naval map (all players on different islands). One of my opponents fortified all of his coast in all the places where one might land units (walls, behind them towers and fortresses). Lots of archers and chariots for defence.
I built several of the large catapult ships available to the ptolemies, meaning to break the defences in one spot to permit landing. But apparently the archers are outranging catapult ships (even when standing behind the walls, it seems).
Of course one can play with rules and say walls are forbidden, but balancing-wise that's still an issue - those catapult/siege ships should be able to outrange landbased defenses, including archers. If you can't clear out a landing spot, its (nigh-)impossible to break the defense. I've tried several times with ships + eles + hero + soldiers (then again I am not a very good players but still...). When there is only very limited space to land units (because of the inability to make space by destroying defenses), you are forced to land your units in a trickle and the enemy can pick them off 1 by 1.
For the overall gameplay, i do not see this creating other balancing issues (like for example the whole skirmish cav discussion), and it seems reasonably easy to change (I admit I have no clue about the technical aspects of programming ;)).
Long story short: I think for balancing purposes the range of heavy warships with siege weapons should be increased to a level that is beyond any other unit or building, with the exception of catapults...