I hated them for ages, friendly AI seems to be really complicated for programmers, it's the worst of the lot, I guess because they partly depend on your own actions, which are never 100% predictable. Mass Effect 2 had really good friendly AI (probably the best I've seen), but it followed the golden rule - it's ok if they die 
Really that's the biggest problem with it. If a companion is someone/something you have to babysit and protect at all costs, they're pretty much automatically annoying. There's also the matter of them getting stuck in something, but it seems by now most devs learned to put a line in of "if companion on follow & x yards away => teleport companion to player" which pretty much solves it for the most part (although ofc if it happens too often, it's irritating, but it's been less and less of an issue). Partial player control also generally makes them a lot more useful (one more cheer for Mass Effect) and eliminates that "just a brainless idiot following me around" aspect (which would probably mostly disappear with good/perfect AI but we're not there yet).
AI seems to be one of the least developed gaming aspects though and I think we can expect some advancement made there, it's just a matter of time before someone revolutionizes it (though I'm betting the first game that does will suck on most other aspects).
Really that's the biggest problem with it. If a companion is someone/something you have to babysit and protect at all costs, they're pretty much automatically annoying. There's also the matter of them getting stuck in something, but it seems by now most devs learned to put a line in of "if companion on follow & x yards away => teleport companion to player" which pretty much solves it for the most part (although ofc if it happens too often, it's irritating, but it's been less and less of an issue). Partial player control also generally makes them a lot more useful (one more cheer for Mass Effect) and eliminates that "just a brainless idiot following me around" aspect (which would probably mostly disappear with good/perfect AI but we're not there yet).
AI seems to be one of the least developed gaming aspects though and I think we can expect some advancement made there, it's just a matter of time before someone revolutionizes it (though I'm betting the first game that does will suck on most other aspects).