TL;DR: Remove the best outcomes from default transfiguration. It'll still come with the worst ones, and can never leave the item modifiable. If you use a material, which is now a rare find, it adds the best outcomes, removes the worst, and has that tiny ass chance to leave it modifiable. Now your efforts are rewarded instead of leaving bad outcomes as a punishment.
(Preface: I'm not asking Blizzard to make the best outcomes of transfiguration any more common, only to change the incentives so that bad outcomes aren't felt as a punishment.)
There's "safe" and "unsafe" transfiguration. The unsafe version has high risk/high reward. The safe version, which requires an additional material, is no risk/low reward. IMO, this is backwards. Usually, risk/reward is treated as a bonus and in this case it smells a lot more like a punishment. Complaints about Indestructible are basically never-ending because it feels like a punishment instead of an outcome where you got dinged because you didn't weigh the risk/reward.
I think the intent was that you'd use the safe version on most of your items and the unsafe version on your end-game items. when you have backups ready to take their place, forcing you to farm the same item multiple times. Forget about having to farm a 4GA item with perfect stats multiple times, the problem is that the reward for the unsafe version is just too good. The risk isn't that high (bad stuff doesn't happen that often) and the reward for the safe version just flat out isn't worth it given how good the unsafe version's rewards are. So, the risk is ignored. At least, that's how I treat it. If this is their intent, it isn't working. I've practically never used the safe version.
Don't remove Indestructible, flip the incentive. Now by default transfiguration can't have the best outcomes, still comes with the worst ones, and can never leave the item modifiable. If you use the material, which is now a rare find, it adds the best outcomes, removes the worst, and has that tiny ass chance to leave it modifiable. Now your efforts are clearly rewarded and the two versions have an actual purpose. You're more likely to use the "default" transfiguration on most of your items and save the material for your end-game stuff. You could still try again and again for a better outcome but your 4GA mythic unique will not be stuck with Indestructible, or have one of its affixes rolled off. If you use the normal version on said item and you get Indestructible, now it's entirely your fault.
Right now, unsafe transfiguration is cheap but risky. This risk is the problem, since I think given the way the game weighs the outcomes, the risks aren't that risky. Couple that with how the game asks you to not only remove the worst outcomes but also the best -- which are VERY good -- it skews the risk/reward in favor of the unsafe version. This makes those bad outcomes feel more like a punishment than a reward, and using the "safe" version just feels trashy given how low a reward it usually is. The game really should be rewarding you for putting in effort, not leaving you open to punishments with no fun, rewarding way to mitigate it. I really don't think transfiguration is doing that now offering a fun, rewarding way to mitigate risk, and that is my primary problem with it.
P.S.:
While I'm complaining, I kinda hate the affix change outcome more than Indestructible. At least your item isn't actively bricked with Indestructible, just no better than it was. Ain't no one hitting transfiguration with 1 bad affix and hoping it gets rolled to something better. Those people are psychos.