I would streamline everything and stick to what works, do it, and do it well. I would take cue's from Activision, as horrible as that sounds:
Final Fantasy: Create two teams to make games, each with a 3-4 year development schedule. 3 FF games should be done each gen. I would scale back of graphical and CGI goals, and focus on classic gameplay, style and setting. Worlds would vary in style between FF4,6, 7 and 10. Some classic fantasy elements but occasional modern tech. The two teams would make different styles, with one very focused on "classic" final fantasy. I would try my best to get sakaguchi and uematsu involved in some way on at least one of the teams. Budgets would be tightly enforced with resources spent on substance over flash. If Xenoblade can be made with a fraction of the cost of a modern FF, a FF can be made in the same way. It just takes talent, and I would seek out talent if need be.
Dragon Quest: Like FF I would possibly have two team, or maybe just one that would release on years that FF did not release. No more online stuff.
Tomb Raider: Laura would get her big boobs back. Screw realism. Tomb Raider should be total male fantasy, with Indiana Jones action mixed with outrageously big boobs. Lots of jiggle.
I would use existing online expertise and resources to develop a new online fantasy game. It would be a total new ip having nothing to do with FF and DQ, which would be totally offline. This new universe would focus on mobile and PC, and possibly next-gen systems. A total new theme for a new generation of gamers.
The main console games would be multiplat, and that would include Nintendo. I'm pushing low cost over high graphics here.
