First off, I consider the 3D remakes entirely different games than their 2D versions. So FF3 (3D) and FF4 (3D) I don't and will not compare to the pixel remasters.
Now to answer the question, There are three games where I miss the extra content. I miss the extra content in FF1 and FF2, it really extends the gameplay for both and in FF2's case gives it a much better ending.
I also miss the extra content in FFV. Due to the extra jobs and end game dungeon. Gives you additional incentive to play and explore more.
However, all three of them play and look considerably better in the pixel remaster than in any release before.
The only game where I am actually torn between the PR for it and another 2D version is FF4.
The PSP version of 4 is incredible, some of my favorite sprites (both boss and player character) as well as great arrangements of the music. The gameplay and magic effects are also spectacular.
But the PR version of FF4 is good in a lot of ways too but I'm not sure it's better than PSP. I'm just not
Edit: FF3 has literally never been better than the PR. Considerably better game.
FF6 is great and the latest patches has helped the world map stutter considerably. It might be my favorite version now. I also didn't care for the "advance" extras, so not a big loss in my book. I feel the translation still allows for Goofy evil sadistic kefka Like the SNES translation without being stilted and too dry like the GBA version