1) Greatly increase movement penalty for going waterborne, something which reflects an army sitting on the coast for an extended time, cutting down trees, building/procuring ships, etc. Perhaps requiring them to sit still for an entire turn to go to sea; no land movement allowed prior, no sea movement allowed til next turn. Meanwhile on subject turn, the army is in an increased vulnerability state, similar to "forced march" mode.
2) Substantially decrease transports' at-sea combat capability, perhaps to the point of nearly eliminating it. Bottom line, a fleet of true warships ought to be able to destroy any similarly-sized fleet of transports with impunity, and to be at least on even terms against a transport fleet 3 or 4 times larger. Right now that isn't the case.
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