Yeah, they do make sneaking a rather pain in the ass...definitely do NOT have a companion if trying to do quests for thieves guild or the like
Oh, for pity's sake, this. ^^^ Last night I did a quest where I was forced to take two companions with me. Okay, fine, I have to take you - and you don't have a "shut up and stay here" option - so try to just follow my lead. I sneak up on the enemy compound. We are out numbered and our enemy is fairly tough. I draw back my bow to snipe one of them and one of my companions says, "What's that? I think I hear something!" Then she charges around me and into the compound.
To make matters worse, Bethesda has timed them perfectly to charge across your line of fire just as you release your arrow. And if you hit them enough, they turn and attack you. There I was, trying to complete this fight off three enemy, when suddenly one of my "companions" charges in, gets hit a couple of times, then turns on me, too!
Egghh!!! This quest was truly annoying. And the thing is, it's so easy to fix: just add more options to companions so they can sneak, used ranged weapons, etc., I had to replay this quest at least five times, just because of these two freaks.
And it definitely effected what I thought of their organization!