To go back to the premise of the OP, I think that Automatics are touted as generally the best firearms skill because they cover such a wide variety of shooting situations. You can use a Machine pistol for up close work, or an assault rifle for your kick-in-the-door on the corps runs. And for what's that's worth, it's true, but I think it's unfair to judge machine pistols on situations to which they're not geared for, namely posing as average Jane wageslave to sneak into a corp. For that, you really want to stick with tasers or holdouts, and it could be wise to add skinflaps, etc. to even do that work. Your machine pistol will do just as well as a heavy pistol for walking around town, but I wouldn't want to try boarding a plane with either.
If you're running, or in, a game that relies on a lot of subterfuge, then pistols are probably king. If you're running, or in, a game where subtlety isn't very useful, go automatics, and if your game is a mixture of the two, then it's probably a good idea to invest in multiple firearms skills -- or beef up your unarmed combat skills.