So given this, the question "which one do you want to write?" is about more than just the story.
You've accomplished something huge: you finished a book, after spending a lot of time on projects you've later abandoned. This is an impressive thing, and you're rightly proud of it, in addition to being nervous about the reception of the end product. Given your focus on work ethic and maximizing chances...would you feel similarly accomplished if you finished another, totally unrelated book? Or would it feel like a bigger accomplishment to complete the sequel that's rattling around in your head?
In terms of circumstances...if you're looking to land an agent, then having an unrelated MS in the works is not a bad idea, just to hedge your bets. On the other hand, sometimes having a sequel, finished or in progress, can be an enticement for an agent as well, especially if they see series potential in the book you're querying. I've heard of it going both ways.
My story: I ended up with an R&R merging the book I was querying with the sequel I'd drafted. I'm no longer with that agent, but not because of this. I'm glad I had the sequel finished enough to make it all work. How unusual my circumstances were I don't know, but one thing I've learned is that everything happens in the publishing business, sometimes all at the same time.