My vote goes to Heroes 3. As Ian already mentioned, the Heroes 3 Complete, which includes WoG, is as good as Heroes can get. Good units, good heroes, and a lot of options to customize your game. And it has a lot of things that was implemented in Heroes 4 like units can move on their own and things. Those were actually the improvements of the fourth game I liked.
But Heroes 4 was seriously flawed in my opinion. And the flaws were exactly the abundance of RPG elements. The heroes, of whom you could have more then one in your group, were so seriously owerpowered at times, that they made armies unnecessary, in thus defeating the purpose of your cities. And before someone attacks, yes I did play it, I played it for quite some time, Heroes being one of the major hotseat timespenders in the dorm I lived in. And yes, a friend of mine created a hero that didn't need armies to clean up the map. Actually it was a band of heroes: a fighter that can take down 3-4 dragons at once, an elemental mage guy, and a summoner. Besides them, I think he only had 4 or 5 Phoenixes in the group. And that was the major letdown for me in that game. That, and the abysmal music