Zombified Prime sounds kinda cool. They should do this as the finale to either Season 1 or 2. In the 2-parter finale, we should see an epic showdown between Megatron and Optimus (what else would happen?) with Megs being super powered up with dark energon. Prime will get his ass kicked and will fail whatever mission he is on. The world will be in imminent danger and the Autobots will be forced to retreat without Prime.
While regrouping, their will be the standard despair and discord from now being leaderless and the usual pep talk that get's the bots right back on track (I would like to see a prime version of either Ironhide or Jazz take command. Maybe even a grizzled vet with a burr on his
rotator)
As they stage their last stand, the Autobots may take a couple of additional casualties but will turn the Decepticons back. In the last moments of the episode as your cliffhanger for next season, we see Prime in a lab/torture chamber being experimented upon in a similar way to Cliffjumper. The end result will be Prime being brought back as "Nemesis Prime," a cannibalistic half-dead monster with the only way to restore him being through a quest to recover a historical relic capable of neutralizing dark energon.
Not sure if this would be any good, just one theory of what could happen if Hasbro ran out of ideas to end a season. (Note the similar circumstances in the G1 episode
Dark Awakening - Difference being G1 Prime could fight the evil influence)