If you have been to Kuala Lumpur several times, its not a bad idea to visit Penang this time round. Penang may not have the Petronas towers nor the best beaches,but it has its own "old world" charm which I have always found refreshing being a KL resident.
There is no doubt that the Shangri-la Rasa Sayang is very popular amongst tourists, but if I understand your post correctly, you will be spending a few days at Pangkor Laut.
Pangkor Laut (Emerald Bay) has one of the best beaches in Malaysia. The setting is spectacular and the beach is clean and quiet (being a private beach). Batu Ferringi (Penang) in recent years has been a disappointment, dirty and very crowded which is why I dont think its a good idea for you to stay there.
I think the "new" E&O Hotel (its a newly refurbished historical hotel in Penang) would complement your Pangkor Laut trip very well.