Nagioshi's still from the old guard, but I think his maturity and mentality of getting these new younger teams motivated will only benefit SEGA in the long run.
I anticipate a new SEGA if it means retaining their unique style of games whilst adapting to the new market in terms of what gamers want to see from them. SEGA can still make games that appeal to the masses if they pull out all the stops to show the gamers that they have a market strategy that is akin to their 1990's adverts.
Personally, I think Nagioshi needs to sort out the whole Shining Youtube fiasco, since I am sure even he doesn't want fans hating SEGA for taking away their rights for loving the Shining Series...it'd certainly assure them that SEGA doesn't want to punish a segment of their fanbase who could potentially go to Nintendo for their SRPG fix.
I know it's not exactly his fault as to why that happened, but since he controls SEGA's image on an international scale, he could calm the debate as to why SEGA did that.