There are several episodes that have enormous plotholes. I noted all of these mentally as I went through the show but the only one that comes to mind now because its so recent is the Scarran threat to Earth - they don't have wormhole technology but they can somehow navigate a wormhole to a specific place and time (Earth) without becomming goop like all of Scorpious pilots. If they can do all that what exactly do they need from Crichton?
I don't like Jool, does anyone? I don't like Stark. D'Argo can get very annoying.
I very much enjoyed the character of Crais, both as a PK and as Talyn's pilot... my problem is that those are two entierly different characters. There was no transition from one to the other. One minue Crais is insane with anger at Crichton, snapping the necks of his Officers, then as soon as he's found out by Scorpius he becomes a reasonable, charitable animal lover. This guy spent years and years as a PK trying to create Leviathan gunships, then he has his change of heart and becomes worried that his Leviathan gunship is too violent and he wants to remove its weapons. Inconsistent.
Crais isn't the only inconsistent one. For a very long time, too long, the first two seasons I think, the characters all went from being friends one episode, to selling each other out and abandoning each other in the next episode. Then they would be friends again in the next episode and you'd think it was a learning and bonding experience for them... but in the next episode they would all be screwing each other again. This back and forth made it difficult to like the characters because for a very long time they weren't likable. I'm not talking about Rigel because he did that up the very end, its mostly D'Argo and Zhaan.