annie's strengths are in her lane poke, burst, aoe CC and in her roaming ability having what is basically an instant stun alongside useful burst.
what were annie's weaknesses last time she was popular and caused her downfall:
- annie is squishy and immobile, this made her the gank target of early laning and an easy target for picks in the mid game from champions like Syndra, Zed, Ahri.
- morgana completely nullified her purpose in lane with black shield and it suddenly became very apparent that hyper carries were surviving lane quite easily with morgana around and assassins nerfed.
- champions with equal harass but sustain on top of it like Nami and Sona made annie's work harder and in turn their ability to disengage fights with ults made annie's flash stun negligible later on.
- Zyra was one of the harder supports for annie as Zyra too was a high burst support with CC, she also had disengage and outranged her, and outdamaged annie if they ever had a plant up, this punished Annie's aggressive zoning style with her having to dodge large numbers of plants to upkeep her zoning.
- later on she isn't much more than a stun on a cooldown based on her entire rotation.
as burst ADCs (or
) fell out favour as too did Annie she has come back alongside 
"it wouldn't be fair to twisted fate when has to have a very short CD on when he has to use stun/cards)"
you do realise TF's stun card are on a 6 second cooldown after he has used it or let it timeout, i think i am right in saying it is the lowest cooldown for a stun in the game, at 40% CDR it is on a 3.6 second cooldown with a 2 second stun, if it wasn't for the fact you have to scroll through it once to get your stun card, you'd be stunned more than you can move.
"2.) Or have to where after she stuns she has a 10 sec CD before stunning again. "
well this nerf doesn't effect her lane at all, her stun is on a cooldown based on all her cooldowns, in the early game when she has only 3 spells, if she hits you with her Q stun, and then W's and then E's and walks back or whatever, she still needs to cast 2 spells, and seeing as her lowest cooldown spell is 4 and her 2nd lowest is 8, she always has to wait 8 second before stunning again, this means the counterplay you want, already exists, you were just too arrogant to look for it.
annie's stun is 1.25 seconds in the early game, comparable to that of
: 1.1,
, 1.25,
, 1.5,
, 1.5,
, 1.5,
, 1.0. a lot of those champions are melee and use the same principal as Annie, reach a certain point in the laning phase and enter the zoning mission.
the counterplay for aggressive laning is the jungler, the counterplay for the jungler is wards. vision is expensive in the early game.