There are lots of advantages to the '39 scenario, and in some ways makes much more sense for multiplayer.
Most notably, you're saving numerous sessions. Meaning less substitutions. Less confusion. More eagerness to play because everyone is playing their part much sooner. In my mind, this is great for multiplayer because instead of a game dragging on for a month + of weekdays and weekends, you could perhaps finish in 3 weeks to a month at most - the result being you get to move on to the next challenge more quickly and again, bringing more eagerness to play from the pool of mp'ers we have available
Balance. This one is going to be debated till the last player boots this game up on his PC. Namely because of the stubbornness every person develops. It requires players to surrender their notions of what is achievable from the '36 GC and enjoy a multiplayer game for what HoI is: a war game. It puts an immeasurable amount of weight on the side of scale that says "combat tactics". The other side, the "IC distribution/builds" becomes nearly irrelevant in comparison. Again...are players going to go for this? Depends. What do you think?
Historical ! omg, omg, omg. This one is key for me...and most of the players in the MP gaming community that I play with know my position on this one. If you want a historical game.........play a '39 ! Has the best chance of getting your 'historical' outcome. Which still means a lot of fun, because of the nature of the scenario. The pressure on Germany to be the uber-unconquerable-hero no longer applies.
After years of playing 'competitive' multiplayer-since the day's of JGBaxter's HoI Players Association for Hearts of Iron 1- I've discovered it is such a drag to play the '36 campaign with a host of rules. It simply wasn't designed for that purpose. If you want to dress it up with a mod, again, it's your preference. The same still applies, the GC was not made with multiplayer in mind - the only way I get satisfaction from playing the GC in mp these days is to actually make an effort to 'not' go historical and come up with varied results. Does that mean start a BCF from day one? Not usually. Some of my fondest mp games have still gone to danzig without war but the catch is the game was played till '51
So. Quick advancement through games/challenges. Balance and historical gameplay. The feeling of fighting for your life with what you've got - (i.e. using combat tactics to secure victory rather than what you can build). IMO, this makes for great MP.