It's kind of funny to see how divisive the mechanic is, as some people either love it and think its a genius trap, whilst others hate it and want it exiled to the shadow realms. Design wise I think it's a readability issue, since the actual purpose of the beat mechanic is to make the player think about kill order; and the reason why that's important is because it gives another layer of depth to being small.
A potential solution we've been floating around for the post jam update is to make the skellies that you cannot kill have a different sprite to the ones you can, and said sprite changes when you share a beat with them. This allows players to see both what beat they are on, and what beat the skeleton is, without having to walk all the way there to check.
Do you think that would improve it?