To be fair, I've never made (and will never make) a change to the site to make a puzzle "easier to solve".
You have to keep in mind that there is a difference between making a puzzle easier to solve (i.e. providing hints, removing more difficult puzzles from rotation, etc.), and improving the mechanics of puzzle solving (i.e. auto-removing duplicate letters, or auto-copying letters from one box into all others, or auto-shifting the cursor to the next open square, etc.). The only changes I will ever make will be always in the latter category.
All I'm trying to do is to make the mechanics of solving as intuitive and irritant-free as possible. Copying a letter from one box into all other boxes is annoying - so we've automated it. Manually moving the cursor to the next open box is annoying (and was how the site was originally set up) - so now we've automated it. Having to remove duplicate letters when you change your mind on a decryption (or make a typo) is annoying - so we're now going to automate duplicate removal.
Auto-removing duplicate letters is never going to be the difference between someone solving a puzzle and someone not solving it. It doesn't make it easier, it doesn't give a hint... it just removes a minor annoyance that may occur once in every 100 puzzles you solve. Its impact on average/record solve times is almost certainly going to be infinitesimal at best.
I understand that there are often requests made on these forums for functionality that would allow unfair advantages in solving - and you're right to point these out as improper. But to lump this change in with all those others I believe is a bit unfair.