Ship Design: Taiidan ships, especially their strike craft, appear to be designed for atmospheric flight, reflecting that the exiles have had experience with this and not so much with space. The Kushan, on the other hand, have more practical designs that reflect their experience in space combat. Their blocky designs are also more boring, reflecting how their society is very militarized and stagnant. Their default color scheme of grey further reflects this.
Mission 13: There are valid theories on both sides for the Kushan cruiser hulks, so I won’t cover that. The still powered support frigate, on the other hand, is way too close to what would canonically be an independently invented design to have been invented 4000 years prior and could not have sat there, still powered, for 4000+ years. Clearly it was abandoned there comparatively recently by the Kushan empire. There is no other workable explanation for it.
Ending Cutscene: A wrecked taiidan scout is displayed next to a wrecked Kushan interceptor. As, other than the kamikaze scouts launched by the emperor, the empire is never seen using scouts, the taiidan scout would have to belong to the player. Also, a large number of Kushan ships are displayed in another portion of the cutscene with a single Taiidan heavy corvette placed centrally from the viewer’s viewpoint. The large numbers of Kushan ships reflect their numerical superiority resultant of them formerly belonging to the empire while the taii corvette has attention drawn to it due to its position and how it’s the only taii ship visible. This clearly shows that they were intended canonically.
HW2: While for the most part HW2 designs are completely different from HW1 designs, the engines for the Hiigarans are of a Taiidan style and those for the Vaygr are of a Kushan style. As the remnants of the empire were absorbed into the Vaygr, this makes the most sense if the Kushan were the empire and the Taiidan the exiles. Also of note is that the Hiigarans have Defense Field Generator Frigates, which the Taiidan, not the Kushan had in HW1.
The only reason Kushan are considered canon is because Barking Dog made it so and Relic didn’t want to make Cataclysm non-canon. Just about everything points to the Taiidan being the exiles.