For me, I would say there are 3 factors that differentiate Star Trek: Frontiers from Mage Knight:
As you’ve already noted, the Star Trek theme is compelling. You really get the feeling of exploring the galaxy, and the endgame of attacking the Borg (or Khan, in the expansion) makes more sense to me than attacking cities in Mage Knight (which always came across to me as malicious).
Star Trek: Frontiers has a “Diplomacy” resource that can be used to recruit crew members (similar to recruiting allies in Mage Knight), but it also can be used as a resource to win planetary encounters. If, for example, I do not have sufficient long range attack to win a planetary encounter, but I have Captain Picard and/or diplomacy skill tokens/cards, I can win the encounter (sustaining no damage) without having to use Long Range Attack or Attack. Again, the Star Trek theme of peaceful diplomacy really comes alive.
With Mage Knight, blocking is all or nothing; either I block all of the attack, or none of it. In Star Trek: Frontiers, your ships have a “Shield” resource, enabling a partial block of incoming attacks. To me, this enhances your strategic options and encourages riskier play. It also supports the theme, as shields in Star Trek are notoriously leaky when it comes to blocking damage.
My two cents, for what it’s worth.