Yup, that Auto-Cannon. The reason we don't really like it is because its benefit (distribute the damage over any visible targets) doesn't weigh up to the damage
potential of both the Rocket Launcher or the Plasma Cannon. With those latter two, you can potentially toast a lot more enemies than the Auto-Cannon. The Auto-Cannon is more of a clean-up weapon, if you ask me: it can help to eradicate a number of disjoint Orcs and Mutants that are otherwise a waste for a single rocket or plasma beam. But in that sense, it's only a slightly glorified Bolter, if you ask me. That being said, we usually just roll the damage first and then distribute it over visible targets, maximizing its potential that way.
Initially, I think 3 Space Marine squads mean the mission is over that much sooner. Most mission, each team enters its own board section. The few missions where more teams enter the same area, we've felt that the team to conclude the round is somewhat starving for Aliens to kill. That, or overloading that boardsection with blips, which in turn means you can't really flood players once they break the final board section. Usually I distribute about 25% of the available blips per board section. In a recent game, I ended up having to place about 7 blips in a single room since the Space Marine players had already seen just about everything else of that particular board section without actually entering it. As a house rule, whenever a Space Marine player looks into a corridor or room of an as of yet unscanned board section, I sometimes randomly place a few blips within sight, which are by definition immediately identified. My players have appreciated that approach, as it makes visibility lines more important - especially when they cross into other board sections. While it allows a cheap snipe on aliens on other board sections that way, those aliens can also go into hiding behind corners and such, forcing the players to advance and take risks. I forgot to do that random placing in that particular mission, though, forcing me to cluster them in a single room

.
Later on, it equalizes. There have been a few games where I as the Chaos Player actually won the mission because I slaughtered so many Space Marines - and yet, the Space Marines managed to at least accomplish the main goal and score enough points to actually get promoted and such. I guess that's what I like most about Star Quest / Space Crusade: even if it's the Space Marines Players vs. the Chaos Player,
everyone can advance and gain something after a mission. No one really loses, so to speak. I am a kind and generous Chaos Player though, I guess; I don't try my best to kill off admirals. We played the first Mission Dreadnought mission and I ended up sinking 7 Dreadnoughts on the Space Marine players and since one of the Dreadnoughts (4 weapons) only saw the Imperial Fist Admiral in sight, he opened full fire on him - and I nearly killed him

. That player then proceeded very carefully with his Admiral for the rest of the mission, but I decided not to stick it to him in an attempt to really kill him off as that would really be a big setback for him for the remaining missions. I even skipped passed a Genestealer chance card at the end, when they only had 3 Admirals and 2 Space Marines left, since in that mission I'd have to place 3 Genestealers at the same time. While fully legitimate to kill them all, if would also kill the fun for the group as a whole.