There aren't too many things in TAS that throw me.
- the inflatable Enterprise
("The Practical Joker")
- the oversized tribbles ("More Tribbles, More Troubles")
- the fifty foot Spock ("The Infinite Vulcan")
- the shrinking crew ("The Terratin Incident")
- the de-aging crew ("The Counter-Clock Incident")
And yet the latter two ideas were used in later live-action Trek of TNG and DS9...though I didn't care much for them there either.
"More Tribbles, More Troubles" I don't care for at all because it's such a pointless story. On the other hand I really like "The Infinite Vulcan" except for the stupidity of Spock's clone being fifty feet tall.