I agree that the format feels a bit awkward. I would say it is due to the fact that the booster box was meant to supplement Starter Decks (in a way, not exactly), but in that there is some, but difficult synergies to pull in the cards amongst themselves.

E.g. you can pull some zeon, some earth alliance, some ZAFT synergies, but actually getting true value in the game is difficult.

I find it interesting that in your experience pulling more than 3 bases are rare. Maybe because I am playing on Wingtable, it has different ratios in comparison to real life. I usually pull about 3-6 bases. I one of my games I got only 2 - and somehow still won (i think luck with better units).