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I think there was a pivot point following the 2004 season in which Edgar and Olerud retired, and with Wilson clearly nearing the end, where they looked at what they had and made the decision to reload (Beltre, Sexson) rather than rebuild. It's understandable. You had Ichiro and Jeremy Reed looking like your #1 and #2 hitters for the next decade, Jose Lopez was a projectable prospect with ML service time on the books, and Felix was your top prospect and looked like your future ace to build a pitching staff around. Also, it looks like that offseason was when they signed Yuniesky Betancourt, because 2005 was when he broke into both the minors and the majors. So, maybe they had an idea that they were set at shortstop. They also had Raul and Bret Boone on the roster.
I think, pretty clearly, they misjudged what they had at that point. I wonder if they even thought about trading Jeremy Reed at the peak of his value? Bret Boone, going into his age 36 season and coming off a season where he was clearly on the decline but still hit 25 home runs, probably should have been traded. I can't recall if that was talked about much at the time. Maybe they were stuck with the salary? The starting pitching in 2005 was pretty mediocre. Just looking at the numbers, it's hard to imagine that they thought this was a pitching staff that would win a lot of games.
You can look at the next few years and see more mistakes. Clearly, they thought they had something close to a contender, and so they kept trying to fill holes, but they were wrong. What I wonder about is how different things would be if they had passed on the 2004 to 2005 reload and instead committed to rebuilding. At a minimum, it seems like that wouldn't have led them to trade AsCab, Choo, and Jones.
I'm not saying everything I think I need to say yet. There are just so many variables. The one constant seems to be talent evaluation. Even if Bavasi (and Fontaine) screwed up all the drafts, if he had properly understood the value of his own players at the major league level, we would have seen better outcomes.