I'm a little uncertain about your objective here. You say it's time for you to build something better - does that mean you want to build a better bench top for the bench you have, a better chassis for the top you have, or do you want to start from scratch?
It's always hard to tell from photos, but the bench you have looks pretty serviceable to me. If the top is uneven, you certainly want to deal with that. The separations in the glue joints I can see in your photos don't look like they would present a significant problem in terms of the functionality of the bench - though they might, if they're getting worse.
If the concern about the glue joints is mainly an issue of appearance, and they aren't getting worse, then I like Dave Mount's suggestion, below - rout and fill.