I'm almost sure we will have leagues in FIFA 06 RTWC. Just look at EA Sports Legal Notices:
http://www.ea.com/global/legal/legalnotice.jsp
There you will find this:
FIFA Soccer 06
© 2005 Electronic Arts Inc. Electronic Arts, EA, EA SPORTS and the EA SPORTS logo are trademarks or registered trademarks of Electronic Arts Inc. in the U.S. and/or other countries. All Rights Reserved. Official FIFA licensed product. The FIFA Logo © 1977 FIFA TM. Manufactured under license by Electronic Arts Inc. Player names and likenesses used under license from The International Federation of Professional Footballers "(FIFPro)", national teams, clubs, and/or leagues. © 2005 MLS. MLS, the MLS logo, Major League Soccer and MLS team identifications are proprietary rights of Major League Soccer, LLC. All rights reserved. All other trademarks are the property of their respective owners. EA SPORTS™ is an Electronic Arts™ brand.
FIFA 06 Road to FIFA World Cup™
© 2005 Electronic Arts Inc. Electronic Arts, EA, EA SPORTS and the EA SPORTS logo are trademarks or registered trademarks of Electronic Arts Inc. in the U.S. and/or other countries. All Rights Reserved. Official FIFA licensed product. The FIFA Logo © 1977 FIFA TM. Manufactured under license by Electronic Arts Inc. Player names and likenesses used under license from The International Federation of Professional Footballers "(FIFPro)", national teams, clubs, and/or leagues. © 2005 MLS. MLS, the MLS logo, Major League Soccer and MLS team identifications are proprietary rights of Major League Soccer, LLC. All rights reserved. All sponsored products, company names, brand names, trademarks and logos are the property of their respective owners. U.S. Patent No. 6,558,358. EA SPORTS™ is an Electronic Arts™ brand.
The second title is FIFA 06 RTWC (Xbox 360), and it has the MLS license.