Flame Atronachs are the starter summon, it's what you use until you can upgrade as against serious opposition they'll get shredded. Can be useful against a mage/dragon that uses fire exclusively but that is a somewhat rare event.
Frost Atronachs are powerful in melee but very slow and can get picked to death by fast mages trying to keep their distance and using Flame or Shock magic. Archers too can give them a bad time. Plus as mentioned, they are exceedingly annoying to use and have used against you in cramped dungeons as there are numerous passages and choke points they'll get stuck in and block up.
Storm Atronachs are great vs dragons as their ranged lightning attacks are 'hitscan' to use an old FPS term. There's no lead time at all so they'll always hit a dragon in flight, plus lightning damage drains magicka which is needed to shout for dragons - no magicka, no shouts = no breath weapon.