Started playing Transformers Forged to Fight last night which has similar character gathering from souls (crystals there). One thing i found after playing a bit was a super cool feature they have regarding getting dupe characters.
In that game, if you get a dupe it's automatically consumed and the main identical character which you already have gets skill buffs.
So translated here, one would have the option to sacrifice the dupe into your existing character increasing skill levels. Would also help with the perpetual need for more skill shards and a more focused dupe sacrificing process. Leave sacrifice as is in case one doesn't care to power up the main.
Anyways, was a refreshing thing to encounter offsetting the disappointment of dupes, figured I'd share.