I made a list for NCAA 2006 so here is my list for Madden 2006:

NFL Europe during off-season(send 6 players over to play and progress)

Practice squads(5 extra players on your team-not active)

Better create-a-play(option, flea-flicker, custom kick returns & coverages, 120 plays & 15 formation in playbooks by increasing the KB of playbooks)

Import coaches from NCAA

Roster size changes during pre-season(week1-75,week3-65,final week-55)

Improve draft(War Rooms(team needs/best player available), Experts rate draft, compensation picks,trade rights of player you drafted on draft day)

Better owner mode(adjust stadium seating using renovate, sell specific player jerseys, earn money for pre-season home games)

Much larger drafts(350 players should be made available in every draft imported or created by the game. This would allow more players at each position so no more running out of WR's by the start of the 3rd round, again just increase the KB draft class on memory card)

True coach progression(Bonus ratings for coach attributes should be given for division champs, conference, and Super Bowl champs, only minor changes to a coaches abilities should be seen over say a 10 year coaching period-(EXAMPLE- Mariucci 84 OFF at start- even if team struggles every year after 10 years he should still be about a 79 OFF, with current system he would be about a 60 OFF conversely even if he won multiple SB and had top offense he should only go up to about a 90 OFF)

That is my list of madden 2006 wishes