I don't see Heisey being a better defensive CF than Stubbs by any margin. There is minor sample size out there for Heisey in CF. IMO, from watching, Stubbs looks much better out there, which seems reasonable considering their athletic attributes.
I still feel that assuming Stubbs' BAPIP regresses, that his overall game is an upgrade on Heisey. At his best, Stubbs has posted 4 WAR seasons, something that Heisey has not shown in CF.