If you're a terrible, inexperienced League player... facing Zyra (especially mid)... you will cry OP. If you're an experienced league player, using a champion you're decent/good with... you will do just fine. Most of the complaints about Zyra's power level come from the lower rungs of the ladder. However, one thing Zyra can do TOO well (i.e. OP)... is the sheer amount of burst she can output on a huge area during a team fight. I don't think a game goes by that I, or another solid Zyra player, don't get at least 1 triple kill. This capability vaults her deep into the AP Carry role. Tone down the total damage potential for that AoE burst, and she'll be just fine.
My suggestion would be: Tone down her ult's AP ratio to .6 or even .5, and see if that brings her into balance, as compared to other AoE AP Carries.