While there were complaints about the games being ports, I think the ones complaining the loudest were people that didn't like the games to begin with. It's not like NBA 2k6 needed an overhaul, and MLB isn't anywhere near the worst game ever created that some some people make it out to be. To me the most glaring area both NCAA and Madden lack in is player interaction because so many aspects of the gameplay are derived from that. With that being said, while the player interaction in NCAA was lacking, it was still far better than what was being done in Madden current gen or in Madden 360. Which is weird, because I've always felt NCAA was the one game you could say is still using the original PS2 Madden engine, where Madden seemed to make a significant change the year they Michael Vick'd the game up (2004 I think).
In NCAA 2006, you had the most responsive/intuitive control ever in a football game imo (including 2k5), as well as better animations than in either of the Madden games. I wouldn't have minded seeing them 360 that engine up (even though it's been around for ages), since they decided not to make player interaction a priority with the Madden 360 engine.