What did he do that was so massively different from most rebuilds? He built up the farm system and once the core prospects were in the majors, he started signing free agents and using the prospect surplus to add big time pieces. It’s not that different from most other teams; he just has the balls and ownership approval to throw the kitchen sink, the bathroom sinks, and all of his neighbors’ sinks at doing deals.
Among other things, he's a lying crapweasel who has knowingly jammed injured players into trades without disclosing their medicals. He tried to strong-arm Hosmer into waiving a set of rights he had specifically negotiated to avoid the exact situation Preller was trying to get him to waive into.
What farm system did he "build up?" His entire "development" system is a hype machine that consists of a pump-and-dump strategy. Seriously, he couldn't get better hype for his prospects if he owned Fangraphs directly. Every year they San Diego has a raft of top 100 prospects. Where are those guys now (aside from Tatis, who was not a Padres signee)? How many players do the Padres have that they originally drafted/signed and developed the whole way up?
His entire strategy is based on bloviating, empty bravado and overspending. He's a used car salesman who thinks he's Warren Buffett.
If he's so smart, why did his rebuild take eight years (and counting?) and cycle through four managers? Well, one reason is that he began it by trading not for prospects, but by trying to accumulate every shiny thing he could, just like he always does - just look at his winter of 2014/15, during which (among other astute moves) he traded Joe Ross and Trea Turner indirectly for Wil Myers, who he's then paid $83 million for...well, not exactly being Trea Turner. That was the same winter he traded Yasmani Grandal plus more for Matt Kemp, Max Fried plus 3 more prospects for Justin Upton, and... well, notice a pattern of trading away guys who became critical parts of championship contenders (and two winners) for other teams? How'd that next season go for AJ the Genius?
Yes, I know I sound semi-unhinged, but it's mostly because (1) I am and (2) AJ Preller is an awful general manager. Yes, he made a couple good trades. With the volume of trades he makes, he was bound to win a couple of them. But he traded critical parts of two World Series champions (with different teams!) plus a pre-arb catcher who immediately made the All-Star team and put up 10.4 WAR over next 4 years away IN ONE OFFSEASON...and then went 74-88. It's a rebuild from the dumpster fire he created!