The Mega Map, in itself, actually makes conventional attacks harder (it gives some of the superpowers more territories and light blue seas, and it gives many territories defensive bonuses). The way to make conventional warfare more feasible is to use High-Tech Edge for Conventional Forces, which reduces the resources required to move forces and increases their lethality, and Colonial Legions and Merchant Marine, which allows you to buy resources during combat (or other parts of the turn). Both of these things eliminate the stalemates caused by the 12-unit limit on resources.

One thing to be careful of, though, is the High-Tech rules--if you use them, you need to use all of them, Strategic as well as Conventional, and preferably the Neutron Bombs and Killsats techs, too. With just the two Conventional technologies it's too easy for one person to get ahead in both tech levels, and after that there's no catching up to him unless he stops researching (because there's no way to accelerate technology, other than buying it from him).

Another couple of concerns: don't allow the transfer of military technology to industry--it's incredibly valuable (much more so than its real-world equivalent), and it also makes the neutral territories essentially worthless (you don't need the extra resources).

Another thing you need to watch out for is a trick that allows you to drop one high-tech army unit by air assault into a territory and kill all the units there using its extra die from the tech advantage and the high-tech edge points, though it's sure to be killed itself--but a follow-up attack is simple. For this, I suggest limiting the damage a unit can do in a battle in which it's killed itself--maybe on a proportional basis (i.e., if it receives enough damage to kill it twice over, it only does only half the damage it normally would to the enemy units).