(Hey, I love flying capital ships in the X games. :B)
Now this is entirely speculation, but from what I've read and the couple pictures of what may potentially be the player ship that I've seen it would seem to be a bit more involved than simply limiting you to your starting ship.
Suposedly the ship is upgraded through the plot, for a start (changing its appearance), but you can also remotely control other ships. But for me what may make up for the lack of being aboard another ship is this:
Player Ship
Only one player ship!
You can move within the interior
It has a cockpit & crew
It is altered throughout the plot
If my understanding of this is right, and my estimations on the size of the player ship (seems M6/M6+ ish?) are anywhere close, there may be a chance that one reason for Egosoft limiting you to one single ship is because they plan on, instead of simply adding a cockpit, adding the entire ship interior along with a crew.
If this is the case, then I'd easily be able to let the lack of being aboard other ships or capital ships slide, since you would get a much better feeling for the scale of the ship you're in. Could be kind of like, using Star Wars as a reference, flying a Star Destroyer limited to being up against the window vs flying the Millennium Falcon with access to the whole ship. One is huge but can feel small, and the other is small but can feel huge.
This is, of course, largely speculation but I can't imagine Egosoft would get rid of such a fundamental feature of the X series without replacing it with something more spectacular than a simple modeled cockpit. Also, as far as modding goes, if my speculation turns out to be entirely true then there's a chance that modders may be able to put together their own ships and ship interiors for the players to move around within. Who knows. Either way, here's hoping for awesome!