None.
Those Dalek voices... I mean, I love this story, but they throw me off every time. It's no wonder they dubbed them in the special edition (though I do feel sad for the original voice actors). Also, the first cliffhanger where the Daleks are revealed to be in charge of Earth does lose quite a bit of impact by the title having the word "Daleks" in it.
Pertwee shooting an Ogron in cold blood is an obvious one. As is the toe-curling obviousness of there only being three Dalek props when they're trying to pretend there's more. More creative direction was needed in that final siege.
What else...the international crisis being represented as nothing more than the Brigadier fielding lots of phone calls. And then just a couple that come down purely to personal taste. I really dislike the scene at the beginning with the Doctor and Jo suddenly appearing from the future. It's a total waste of time; and the plot itself (though original at the time) is for my tastes just a bit too typical sci-fi. I feel like Doctor Who could and perhaps should be coming up with something a bit more, again, creative. And the final thing is ridiculous, but it really is indicative of this era's indulgence and distance from the original vision: the Doctor swirling, supping, and indeed assessing, wine: Hartnell "never touched the stuff". In my opinion Terrance Dicks and co. no longer have any interest in the Doctor as a role model to children. He's a hero to the writers instead. And that makes for a much less likeable programme.
Pretty much everything to do with the Daleks. Their comically unthreatening and lame sounding voices (would it really have been that much trouble to bring Peter Hawkins back?), the fact that they contribute barely anything to the story to begin with and feel like way less of a constant presence in this Dalek-ruled dystopian future than they really should, and the really underwhelming assault on the government house in the climax (I know the show would go on to make a point about how even a single Dalek can be a very significant threat, but having only three Daleks take part in what is supposedly an assault to ensure their future as rulers is still pretty damn weak). It just makes for a really lame and underwhelming season debut and a comically awful comeback for the Daleks after five seasons in absentia. I don't even think the Special Edition improves things as much as people say it does, and I really think this story would have been better off without the Daleks as it had initially been written.
What do you think?