Can Proteus Isis open Eagle's schematic?
Your question has two parts, the fist part (best software) is a matter of preference so there is no point sharing my personal opinion although I don't see why it is a problem using both and you need to choose one or the other.

In your second question about importing Eagle files in ISIS (schematic) or ARES (PCB) this is not possible, at least up to the current version 8.