The issue of transport links with the Isles of Scilly is more involved than just the air link and personally I think the solution should be a joined-up one. Separately Penzance town has been debating an updated sea link for some years.
I think the two could be combined to form an imaginative and coordinated transport terminus based on the already existing rail and bus stations, with Albert pier alongside. To this site I would construct a Helipad on reclaimed land outboard of the waterworks and adjacent to Albert pier. There would need to be some serious dredging of the seabed on the outer wall of Albert pier to accommodate whatever vessel replaces the Scillionian III, no mean task as the seabed there is blue elvin granite. The helipad would enable touch and go of a smaller helicopter (perhaps a 15-20 seater, thoughts anyone?), which would be based elsewhere (say, Newquay, or Culdrose). Freight for the IoS could also arrive by rail direct to Albert pier (as it used over 100 yrs ago - the rail lines still visible in the surface).
Plenty more details to discuss, but the principle idea would be a coordinated and imaginative transport terminus that would benefit all, particularly Penzance which really could do with an economic shot in the arm rather than the kick in the crutch it could do without, as well as some of the 9, yes 9 supermarkets the town now boasts.