Have you already checked out Cour des Loges? I have only been thru the lobby, but this hotel certainly had a lot of buzz at the time it was opened. It is ideally located in the Old Town. That would be my preference, unless research on it turned up a lot of bad reviews. I love the location - walk outside, in the heart of the old city.

I've stayed at the Hilton Lyon twice. It's fine. It's a big conference hotel that treats its Hhonors guests well. There is a trolley line just outside of the hotel on the park side that takes you into town quickly and easily.

Here is a recent thread you might find useful.

Here is an old thread on the topic.