Dragon Quest does not, not really. From the onset you're told 'Go killeth yon Dragonlordeth' and the Dragonlord is indeed the final boss. You could say his second form is kind of a surprise, I imagine it was at the time. Every single battle is one-on-one, but then you beat the Dragonlord and a second fight starts immediately from within the same battle screen. So for posterity's sake it sort of counts.
Dragon Quest 2 has you set against Hargon for like 99% of the game, until oops, turns out the baddie is Malroth! This is a literal last minute bait and switch, so it's not like there's some final leg of the game where you're focused on Malroth (maybe in the upcoming HD remake?) but still, it absolutely counts.
Dragon Quest 3 is where the pattern really coalesces. You spend the vast majority of the game dead set on killing Baramos. You explore the entire damn world so you can kill Baramos. There's nothing left to find once you get to his castle. But then you kill him and, whoops, turns out the real big bad is some goober named Zoma, and you get sent to a whole other (familiar) world to fight him there!
Dragon Quest 4 has a little bit of back and forth between its two main baddies. You encounter, or at least hear of, Psaro fairly early on, but eventually your focus becomes taking down Estark. But once you do that, Psaro steps back up to be a NEW Estark! Bigger! Better! Green! Psaro is the first villain in the series to to have more to him than 'hurgh blurgh monsters rule humans drool!' and that's memorable, but in the end his first form is just another Estark. So does he count as a bait and switch? I'd say so.
Dragon Quest 5 almost certainly has a clear three-act structure with each act break punctuated by one tragedy or another. But you still spend most of the game being pursued by or in pursuit of Bishop Ladja. It's not until you put him down that it's revealed you actually have to defeat Grandmaster Nimzo. And that ridiculous name is only the second most memorable thing about him. The most memorable thing is that he is literally a Namekian.
Dragon Quest 6 opens with the main hero and companions trying to defeat Murdaw, and he's the main focus for the first part of the game. But he's taken out relatively quickly compared to the other 'first baddies', but then there's a period where other equally powerful demons pop up, but eventually it's revealed that they're all working for this dork Mortamor. There's a 'sort of' post game quest you can do, but canonically it takes place right before you kill Mortamor so Nocturnus isn't technically another new final boss. He does kill Mortamor for you though if you beat him and I always liked that touch.
Dragon Quest 7 breaks the pattern because there isn't really a fake out first villain. I mean, there kind of is, I guess? You eventually learn Orgodemir is the baddie, but then you kill him. So, new baddie then, right? As it turns out, no. Orgodemir pretends to be God The Almighty for a hot minute before dropping the pretense and just becoming the final boss. I might be misremembering some sequence of events, because I stalled out on my 3DS playthrough and I only played through the PSX version once when it came out (checks notes) over twenty years ago. Oy.
Dragon Quest 8 has you spend most of the game on the trail of Dhoulmagus. (Or Dhooooooooulmagus according to King Trode) but eventually you corner the bugger and defeat him, and it turns out that evil enchanted staff he's been carrying holds the soul of the ACTUAL baddie, Rhapthorne. Pretty standard bait and switch here, really.
I never played Dragon Quest 9 or Dragon Quest 10 but I assume something similar happens in those games at some point.