As someone who worked at Square, my impression at the time was that the problem was lower than expected engagement with the order functionality at existing locations, which made it hard to show the value proposition (I didn't work on Order but it was a small company). I'm not sure failing to be a flagship product caused the problem, Square has other products (e.g. Caviar, which people often don't know belongs to Square) that have succeeded. This despite Order having a decent UX and some interesting features like arrival prediction.