How to avoid making annoying villains

*SPOILERS FOR MASS EFFECT 2 & 3*

In Mass Effect 2, Cerberus is introduced (ignoring their irrelevant presence in ME1) as a pro human group that are okay with fairly ruthless methods to enhance the interest of humanity, even if that's at the express expense of other species. But not exclusively, there are plenty like Kelly Chambers who love aliens, she just supports humanity first and them second. It's a nuanced concept that can't be hand waved away in an instant.

In Mass Effect 3, they are sort of reduced to just 'bad guys'. They pop up around the place causing trouble and frankly, don't have a compelling reason to other than 'mwa ha ha'. This makes them annoying and a nuisance, rather than interesting and fun.

What are some ways in writing that we as authors can avoid making our antagonists 'annoying'?