Well...

If you'll recall, we needed Matoya's Crystal Eye to try and find Minfilia after she was caught up in Y'shtola's Flow. Unlike in I where it was literally a crystal eye Matoya used to see, this one was an artifact of immense magical power - a Crystal of Light from a bygone era. It's much larger and more powerful than the ones the Warrior of Light possesses, from which it can be surmised that Hydaelyn was indeed more powerful in the past than she is now, and that primals and Calamities are to blame for her weakening.

As to whether aether can be replenished or once it's used up is gone for good? Well... thermodynamics disagrees with the former, but given this is a world of magic that might not apply. There's no conclusive evidence one way or another, but it's best to err on the side of caution.