For Morello, some points:
- The AP ratios on her abilities are fine, and in line with similar abilities from other champions. Her Q is actually weaker than a Cassiopeia Q because of its scaling, but match it with hits from her plants and it's still in line with Cassiopeia getting off a few Es after landing Q.Her E at .5 is fine.
- The mid-game scaling on her plants and passive could use a nerf (the nerf on multiple plants hitting the same target is moving in the right direction... maybe they do a tad bit less damage for consecutive shots? So as their health bar declines, they do a bit less damage? Not a huge amount less, but it's worth a shot)
- The number one thing that made Zyra broken is when you gave her inherent 20% CDR. With blue buff and masteries, she has full CDR just by getting W to rank 5 (usually at level 18 for most Zyra players). Now, WHAT DID THIS DO?
Well, it means that you don't need to build CDR on Zyra. Ever. Just by reaching level 18 and having blue buff, you have full CDR. That means that you can spam your abilities like nobody's business (plants and roots coming out all the time, making her play like a Cassiopeia w/ spammable harass). Before she had this CDR (and I remember it from playing her on PBE), Zyra players had a choice to make: either build CDR and sacrifice some damage to be able to spam for utility and sustained damage, or build full damage items and manage the use of your spells better (with the obvious tradeoff of better damage). You can build RoA/Rylai's/Deathcap/Void Staff/Zhonya's/Sorcerer Boots and know that just by hitting level 18 and having blue buff (which is likely since you're probably the mid mage), you'll be able to spam your abilities as if you were Cassiopeia.
By removing the 20% CDR, Zyra players will have to manage the use of their abilities in teamfights better (versus spamming with no fear of cooldowns) and build their full damage items, or build CDR and go more of the way of a utility mage.
You said a while ago that she's a combo mage, kind of like Anivia. Giving her so much CDR inherently (and thus the ability to spam, as I have mentioned) makes her a combo mage with Anivia burst on a very short cooldown. THAT is why she is broken.
tl;dr: From someone who loves Zyra, all she needs is readjustment on her mid-game scaling and for you to get rid of that 20% CDR on her W. If she's going to be a combo mage, don't give her the ability to spam that combo like a sustained DPS champion like Cassiopeia.