My 'good guys' were a mix of Space Marines, Imperial Guards, Adventurers, and Eldar (including Harlequins) and these fought against the 'bad guys' of Orks, Chaos Renegades, Adventurers (sometimes the same characters who were notorious for switching sides), and Genestealer Cult forces. The games were usually small with 20-30 models per side (sometimes unpainted, did I mention that before? Shudder!) with limited vehicles - I had a rhino, a landspeeder, an Eldar Warwalker, several Ork buggies, an Ork dreadnought, a Chaos dreadnought, and a couple of robots.
On the first page of the book (well, page 6, but the first page of text) I might have found the answer to why the 1st edition was my favorite...
To fight a Warhammer 40,000 game you will need an extra person called the gamemaster, usually referred to simply as the GM. He will act as the umpire or referee, and it is his task to enforce the rules of the game; interpreting them where necessary. The GM should make sure that the players have sufficent dice, pencils, paper and any other items needed during play.
It is possible to fight a game without a GM, so long as players are willing to cooperate a little, adopt a reasonable attitude and are honest in their record keeping. It is also possible to fight games where all of the players are on the same side against a side controlled directly by the GM. Of course, this does rely on the GM to make the game as fair as possible. One-sided games against the GM should be conducted with the aim of finding how well the players preform, rather than by aiming to defeat them.
How different is this than modern 40k (or Warmachine or Bolt Action or... etc.)!? Throughout the original Rogue Trader book, many of the rules are presented with the idea that there will be a GM to adjudicate situations and interpret the rules as a neutral observer (and I love that one of the GM's duties was to make sure every one had pencils and paper). The book often seems like more of an RPG than a wargame. Now, I played plenty of games without a GM, but the narrative seemed far more important back then than seeking advantages in the Rules As Written, fielding the optimum model to point ratio, or even winning the game.
This aspect of the game was missing from the 2nd edition forward. Certainly you could play with a GM, but that element was not written as part of the game. Again, I'll get into specifics as I sort through the chapters, but as far as what made it my favorite, I can probably stop now!