Well, Dukat's a complicated character. During seasons three through early five, he is often helping the good guys. This isn't because he's reformed or seen the light though. To me, Dukat is a Cardassian patriot. If it's in Cardassia's interests to work with Sisko, he'll do it. On the reverse side of the coin, he has no compunction whatsoever about "betraying" them. It wasn't really much of a betrayal either. His relationship with Ziyal... will definitely be explored more during early season 6 let's just say. He does have a huge soft spot for family, even if his ruthlessness runs contrary to that at times. This is a division within himself that will come to bear.
Jake staying on the station? I give that one a pass. They're evacuating the station quite hastily, under fire, and Sisko's got a lot more going on than just checking to see if Jake followed instructions, when he's clearly a smart guy. I can see it when they're doing a final head count they realize he's not there. It's not like they had time to check roll to see if everyone was on board as Dukat's final attack wave is incoming.
The whole premise of the minefield is, that it's self sustaining(through magic apparently) and can't be disarmed or removed. So now that it's up, the wormhole is closed and the station ceases to be that important. So while the Dominion and Cardassian fleets are committed to attacking the Station, the Federation and Klingon fleets are free to hit some real important targets. To me this was one of the best season ending scenes. The Defiant joining the Federation/Klingon fleet. It wasn't so much a cliff hanger as... a promise of things to come. When I first watched it... it was agonizing having to wait six months for the next season!
Season 6 opens on a real... surreal note too. Dukat's giving the captain's log, Weyoun and Damar are working in Ops. Both of them are excellent characters and will very quickly cease being just background characters. I say Damar even surpasses Dukat in so many ways(to me his character arc is second best only beaten by Nog's). As for never sending reinforcements to the station? Did you forget that Federation/Romulan/Klingon fleet defending the station in By Inferno's Light when Dukat joined the Dominion?
Season 6.. well it starts the war arc which for better or worse really ends up defining DS9 on so many levels. A lot of the best stories are yet to come