First of all, many changes did seem to come around the time that Iwata 'took over'. But I don't think they can all be linked directly to Iwata. Remember, many of these 'sweeping changes' are not entirely based on the financial side of Nintendo. Some were based on the games development themselves. Which were governed by people such as....Miyamoto (main producer and overseer of game development) or the games developers themselves.
Its true, Iwata may have come in and made some grand changes, but he couldn't have changed everything himself. If anything, what you may be seeing is the overall change from Yamauchis approach of controlling every little thing to a more open-ended approach of setting up studios who don't need a watchdog CEO with a red rubber stamp to approve every little action they do.
...and for the most part, this open-ended approach seems to be working quite well so far.
Six upcoming games you should look into:
Essay Pro