Well basically its because Bandai didn't make PC Engine games, and nobody but Bandai makes Gundam games in Japan. Dragon Ball Z is the only Bandai game on PCE that I know if, and it was quite late, 1993 I think. I really like that game a lot, btw.
Also its worth pointing out that Gundam was in sort of a lull during most of the PCE's heady days, and non-UC Gundam didn't exist until 1994, so Bandai was in a different mode than they are now. Now the rule is "always make Gundam stuff, even if its shit", but back then Bandai was still a slave to Tomino, and only made shows when they could fit into his G world.
A *good* Gundam SCD from 1994 or so would have been really kick-ass. It also would have been really unlikely. Bandai makes cool fun games quite regularly now, but back then they made almost nothing but shit, and virtually all of their anime titles were garbage that did nothing to enhance the anime experience. For example, Gundam F91 on Super Famicom.
Something like an Assault Suit series game with voiced cinema would have been great though...