Looking at this collection, I'm suddenly reminded that for the initial 3-packs they came out with (1 TOS, 1 Movie, 1 TNG), the TNG came out with the Borg Cube, the Warbird, and the Vor'Cha before the Enterprise-D, which wouldn't come out until the second batch of 3 packs. What was up with THAT??? Could they not get licensing rights for it at first? Did they really think kids wanted to play with a Borg Cube before the "D"?
I think they were just trying for some variety. As I recall, the first wave of TOS ships was the Enterprise, Romulan BoP and Klingon D-7. The first movie wave was the Reliant, Excelsior and Klingon BoP. At this point, we have three Starfleet ships, and two Klingons. It was probably felt that for TNG rather than include a fourth Starfleet ship a third Klingon and second Romulan, best to give Trek's primary races some more repersentation. And the Borg were a big deal back then, so they were obviously considered worthy of the first wave.
Also worth mentioning, when Playmates did their toys of the ships, their first wave of that was just the Romulan warbird, Klingon Vor'cha, and Starfleet shuttlecraft. The Enterprise D was in the second wave.
The movie Klingon battle cruiser might've looked too close to the OS cruiser to bother
Not really an excuse, considering how many ships of the same class they had like the Reliant and Saratoga, Excelsior and Enterprise B, the Enterprise D and its three-nacelled variant from AGT, a Klingon BoP and an HMS Bounty variant, and hell looking over that picture they seem to have released two different Borg cubes. Now sure in the case of the first three there were design differences, and one Borg cube is a lighter shade than the other, but with ships that similar released, they could have done the K't'inga.