Wouldn't that be a pretty easy fix though? Simply make the transports selected as part of your flotilla be the only ones whose transport value is relevant to the scenarios. So you can take as many more transports as you're allowed in a Rogue Trader fleet, but only six transport points' worth of transports will count, and these can't be changed from game to game. (Their transports are the same as the ones anyone else would be using anyway, right?)
Also, I would like to say I don't find it a problem that the games don't end up being centered around the transport flotilla. I personally don't get to play BFG a whole lot, so I like that the games are more of a regular battle with a bit of a twist or bonus than an all-out break from regular gameplay. Having the transports be the main/only important part of the game makes it feel more 'gimmicky' to me. Also, if you increase the focus on the transports, what are you going to do about the IN NC advantage that AndrewChristlieb mentioned? I don't want to play a game where I lose hopelessly in the first two turns because my transports get obliterated by NCs from across the table.