Well, both Hiltons give Diamonds the choice of breakfast in lounge or in the restaurant (some hotels only allow breakfast in lounge for Diamonds).
Both Hiltons give you a little gift in the room (don't remember what exactly - wine, fruit bowl, cakes????).
Both hotels upgrade if possible (don't expect upgrade to suite).
And in general I just feel well treated....

If you are only walking, Hilton Old Town is definitely the best choice, but if you are using public transport, Hilton Prague is fine - it's only 2 or 3 tram stops from the Hilton Old Town and very close to a metro stop as well.
Look at a map to judge for yourself.