For each major release, HOIs 1-2-3, the best "version" was the last one released. But they were all somewhat different.
HoI-1 was probably the "weakest" as an official release, as it had some key issues that were never fixed, particularly regarding air and naval combat. It had a fair bit of micromanagement, but not too bad. For its time, however, it was an industry changing game, raising the grand strategy computer genre to new heights.
HoI-2 dumbed down the research trees considerably, which some didn't like but most did, and it greatly improved the naval combat system. It also made numerous incremental improvements to the UI and zoomed in the scale a little bit (smaller provinces, and therefore more of them). Many people think that HoI2 struck the best balance between depth/complexity on one hand and learning curve/playability on the other. But it still had little in the way of automation in the UI, and therefore the player had to manually handle all unit moves, builds and combats. But at the scale involved this didn't result in too much micromanagement, or at least such was the general, if not universal, consensus. The vanilla game was good, and each expansion added nice features; but all versions from vanilla to Armageddon were complete, balanced games. IOW you didn't NEED to upgrade to any particular expansion in order to have a good, well-rounded game.
HoI-3 was the most ambitious, zooming the scale in much more, resulting in MANY more smaller provinces and therefore potentially much more micromanagement. It compensates for this, however, by introducing the ability to delegate operations to the AI at any level from corps up to entire theaters. Obviously manual control still provides the most opportunity for a human player to leverage his better brain power to advantage, but all things considered the AI does pretty darned well in most general situations once you realize its quirks and how to avoid/manage them. For obvious reasons HoI-3 is the most complex and therefore has the steepest learning curve. Many less-than-hardcore strategy gamers were not pleased by just how steep that learning curve was. Also, HoI-3 did not become a well balanced, complete offering until you added the Semper Fi expansion; and it did not reach its full potential until For the Motherland. In short, the vanilla release was heavily gimped and had some major bugs/handicaps which were not fixed except in the expansions. That said, the Semper Fi version is very nice, and the FtM version is, IMHO, the best grand strategy WWII game ever released.
Not the most helpful answer ever.
Hehe. Dude, he is the OP, so he is the one asking the question in the first place. ;-)