On what distance are you engaging with the pistols?
Don't have shields yet...
Keep in mind when I say shields, I mean the full-size riot shields that take up one hand, not personal energy shields. As long as you have combat vests or tritanium vests, you can choose to give them a shield which improves their frontal armour by around 15-20 points or so. As such, a shield trooper is completely immune to 99% of incoming ballistic fire, and without the much higher penalties from the full-body armour.
Engagement range for shield troopers is around... I guess I'd say 12-15 tiles? The aimed mode is accurate out to 22 tiles too, but I primarily use snapshots as they're extremely cheap at only 18% TU and have a base accuracy of 80%.
Rookies get put into shield duty; they have a light, easy-to-handle gun and whilst they're considered expendable they're also well-protected and get plenty of opportunities to practice shooting at enemies. If they survive long enough (and so far, they have) they can be quite effective.
Honestly if I had the research done and enough ammo to spare I'd be issuing them laser or plasma pistols instead, but for now the blackops will have to do.
What do you do against aliens? Pretty sure it won't be BlackOps pistols... ^^
So far I'm early enough that I haven't skirmished with them very often, but for the most part the ones I do encounter are
quite vulnerable to ballistics. I'm mostly trying to take captives at the moment though, especially engineers, so that means flashbangs, dartguns, and a lot of luck.
Man, it seems you fell in love with miniguns, so you can't see other options to do. And these options are exist.
A lot of (especially inicial) weapons are useless indeed, but I think that is not a question of poor balance, but the question of variety. Isn't it cool, when you are trying this and trying that and become to the right and lovely tactics by your own?
Basing on my own experience I can't say that any type of weapon has the real and uncounter advantage.
My main philosophical idea: if you'll make everything useful, you'll make this useless at the same time.
I think the fact we have Stats For Nerds makes it easier as well, because it allows us to make more informed decisions than the vanilla ufopaedia would. Things like rounds per mag, nonstandard range values (a very important factor; for instance the BlackOps SMG has much better effective ranges than the Mac10) and so on.
As for weapon types... maybe there's no clear overall 'winner' so to speak, but I'd say within certain brackets/groups there are undeniable best-in-class options. Early-game assault rifles/carbines for instance, I think the FAMAS is probably the best of the bunch - the AK is much too slow and the L85 not as accurate. They're then all largely made redundant by the blackops weapons, which can gradually be phased out in favour of energy weapons, and so on.