There certainly are similarities. Both Thomas and Roseman had an uncanny, lucky, off-season in which everything they touched turned to gold. Both had a problem with deficient pipeline going forward -- Roseman was missing a lot of draft picks from the trades which landed Wentz, while Thomas had inherited both a truly deficient farm and a limited budget, which quickly became impossible with the Daulton/Dykstra contracts. Both Pedersen and Fregosi did well with a lot of vets. Both sort of innovated, with what were established methodologies: the run-pass option and heavy use of platoons. Both managed to inspire their teams to do the seemingly impossible. After Wentz went down, Pedersen won the championship with the untouted journeyman QB.
I've always seen Thomas as a good GM emasculated and then fired by Giles. The Eagles big advantage over the 1993 Phillies is the owner. And to Zambonir: yes it certainly appears that Pederson erred in staying within the org to replace Reich and Diphilippo. The playcalling on offense this year hasn't been up to last season's level and the scripted plays at the start of the game have been a particular negative.