The downside is that you can't use the same six champions for each of the three keys. You need to build an entire set of fully-geared champs for each key, and you'll need to build even more for different affinities.
I guess, that is exactly what Plarium wants to achieve with the Hydra. Once you have done all content, there is no need to build new champs anymore - and that stands for no need to use shards anymore. Players building new champs are players buying shards and books.
I don't think that is bad. It keeps the game alive. I just hope, they don't exaggerate and we can use some of the champs that are good at CB or dungeons as basis for the teams. Building some new champs in addition to our existing teams to clear new content is ok. Building 18 new champs, because no strategy from CB or other bosses works vs. Hydra would be to much.