As you know we're a small team and can't commit most of our development efforts for a complicated feature that is only usable for a small percentage of our players (as I mentioned elsewhere, we have less than 2000 players with 1K+ items). I'm sure you can agree we have other things to add or fix in the game.
We are putting an effort to develop the system that allows conversion to powerkits based on tiers, which is less complicated and still allows you to have control over your items.
The system we chose to go for can actually gives you the same freedom you suggested to keep items you want, in exchange for more manual work on your part. For example, if there is a Legendary item you want, just don't convert the legendary items and manually use all but the items you want to keep as boosting material.