-Its is slow, so you can't rally your first cyclone across like you can do with reapers and hellions, because your oponnent would have way more stuff than you, so you need a medivac to boost across or build up a cyclone deathball.

-Its is cost a lot of marines and tanks to build a cyclone deathball.

-Its insanely fragile even for terran units standards, 110 HP and 0 armor for 125/50, if you have 1 armor(like tanks and marauders have) you can reduce a reaper dps by 24%, and reduce a dps of 2 marines by 30%.

-It doesn't scale, stim marines is just better than cyclones in everyway, they don't get super smashed by tanks like cyclones do, they are better at dropping, they wipe buildings faster and they smash cyclones specially without speed upgrade, and you could have more tanks.

So to counter cyclone you just need to turtle up until you get stim and a health marine count then you just move out with all your tanks, if he tries to badger you with a medivac you siege a tank in your main mineral line right on a missile turret spot, if he tries to drop on top order your scv to clump on the tank untill your army arrive and kick him out of your base