What about perhaps just disabling titans in flagship victory setting? It would give appeasement to any players who are worried or have reservations about the strategic importance of titans, would give the flagship game-mode a bit of a nostalgic classic-sins feel, and frankly the exclusion of titans from a single game move shouldn't be too much of a hit to one of the expansion's shiny new features.
Or better yet, give hosts the option to allow titans, but have the default setting be titans disabled for flagship victory.
Honestly either way I think flagship victory setting will be more interesting without the presence of titans. If the flagship switches to the titan, everyone will have even more incentive to rush a titan. If titans are disabled it adds the additional choice component where the player has 6 choices of which ship to use as a flagship.
Also it's worth noting that titans with the flagship additional abilities might be too strong.