Although I somewhat sympathise with a bit of disappointment that you "have" to buy the Transport in order to get the new X-wing, your arguments are inconsistent and don't hold with market realities. I would love for there to be Card-only expansions, for example, but it seems that this is economically infeasible for FFG to produce, and so I would rather they come out with repaint packs if it means the game continues to grow.
It occurs to me that there is a flip side to your argument as well, though. Perhaps you are right that the Transport woudl not sell well without the inclusion of the X-wing. But it seems that for everyone like you who is disappointed that the X-wing is included only in the Transport expansion, there are more people who would be disappointed if FFG was unable to produce the Transport at all. So if including the bonus X-wing is the only way to induce a sufficient number of sales in the Transport, in order to successfully kickstart the Epic format, then I think a lot of people are happy that it was done this way.
Really, so many people have already addressed the issue of expecting to recoup your money, of preferring random purchases, and of methods for obtaining the parts you want on the secondary market, that I need not add anything else to that.