I guess I see the Thome signing differently.
I've seen the Phillies field seriously competitive teams in three eras now - 1976-83, 1993, 2007-11. None of those teams was built on high-level free agency; the were constructed largely of players developed by the Phillies, and players acquired in astute trades, or picked up as discards from other organizations.
I really don't see the Thome signing as transformative - rather, I see it as pretty consistent with prior Phillies efforts to "play" in the free agent market. Rose; Parrish; Jefferies; Thome; Bell. Some better than others, but nobody who became a long-term core player for a perennial contender.
I see the Thome/Bell signings not as the beginning of a new era - but as the last hurrah of what was, overall, a failed approach. Thome's presence was a positive; David Bell's presence (signed at the same time, in Philadelphia for the same years) was a clear negative. Some argue that Thome's presence held Ryan Howard back, but I don't buy that - Thome only started about 50 games in 2005, and that's not a significant impact on Howard's major-league career. Bell's presence, on the other hand, did steal a full season from Chase Utley, and also led to the Phils missing out on the best years of Placido Polanco's career.