Seven of my top ten worst episodes are from the third season (surprise!)
The Alternative Factor
The Gamesters of Triskelion
And The Children Shall Lead
Let That Be Your Last Battlefield
The Mark Of Gideon
The Cloud Minders
The Way To Eden
1) Metamorphosis (The end was terrible - loss of two personalities by joining them in one is so romantic!
Sacrilege! "Metamorphosis" is a beautiful story. YMMV.
2) The Alternative Factor (pure, gold boredom.
That ep was worse than boring. Muddled plot, incomprehensible science, script padded out with endless spinning starfields and stuntmen fighting in dry-ice fog.
8) Let That Be Your Last Battlefield (Obvious symbolism is too obvious)
It's not even symbolism -- just 52 minutes of preaching.
9) Mudd's Women (It's very happy end for woman who had been washing dishes for her father and brothers for the whole life - to marry wild miner and wash dishes for him)
You're missing the entire point.