Defense is loosely based on Milan - fairly compact and all players were decent to good in possession:
Van der Sar over Buffon is controversial, but there's no other keeper I'd rather have for this scheme given the time-frame.
Maldini for the Abidal type role - where he was more reserved than Alves, and combination of LB + LCB.
Late '90s Stam has the highest peak of any stopper in those 20 years, IMO.
Nesta has to be there - best centerback of the last 20 years - and knows how to cover for Cafú on the right.
Cafú for Messi, plus he wasn't exactly half bad in standalone terms.
Midfield is based on Barcelona/Spain - which was the most dominant one over the given time-frame, and can rival any midfield ever:
Redondo for Busquets in the holding role - he'll have to be a bit more reserved, but is the perfect player for this scheme.
Xaviesta needs no explanation - Zidane might not work with too many stars - but these two can and are synonymous with the style as a symbiotic pairing - from passing to movement to pressing to telepathic understanding.
Attack also loosely based on Barcelona - decent mix of individual and collective brilliance:
Fenómeno + Messi is fairly straightforward.
Ronaldinho over Cristiano - just think Ronaldinho's absolute peak was a bit higher, he's proven in Barcelona's setup (kinda like Rivaldo), and has played with both Messi and Fenómeno (also like Rivaldo).