From our outsider perspective perhaps, but Gedo knows what his primary audience is. He could take national heroes like Sakuraba along with casual fan superheroes like Makabe along with the underdogs like Honma and the purist heroes like Shibata and string the shows necessary between now and G1 and even afterwards.
The whole "Tanahashi won't challenge again for the IWGP Heavyweight Championship" angle from Wrestle Kingdom was a terrible shout by Gedo that he can't be blamed for since, he wasn't expecting Nakamura leaving and was probably gonna swap the two half way through the year card-wise.
Keep in mind that beating a singles champion in the G1 usually earns you a title shot in the string of shows between G1 Day 25 and Wrestle Kingdom and World Tag League further thins those shows.
Right now we've got Best of the Super Juniors where the Heavyweights take a backseat so I imagine we'll get a lot of CHAOS - Los Ingobernales tag matches and a build for Goto as a challenger to make up for Naito losing at Wrestle Kingdom. That match can take place at Dominion, and Naito gets his win back.
Next up is Kizuna Road, which is a B-PPV last used to promote Prince Devitt. If we go by that example, it'll probably be a Katsuyori Shibata challenge there that Naito retains handily.
Post Kizuna is the G1 and the G1 gives Gedo all the opportunities he needs to make guys challenge Naito in it's aftermath, and he'll probably drop victories to Makabe and at least one other wrestler there for after the Climax, not including Okada for Wrestle Kingdom.
Makabe is actually a very major babyface in Japan with casuals, so he's a lock to face Naito at Destruction while Tanahashi carries the other Destruction card (if they have two like last year).
After Destruction there might be some UK events to pad out the year, and then we're at King of Pro Wrestling. KoPW usually features title rematches, so if Naito hasn't dropped the title here we might see a second challenger pop up from the G1. I'd personally pop for Kazushi Sakuraba since he's a national hero in Japan and beating him clean in the main event only furthers Naito's year, especially if Kazushi submits him somehow in the Climax. Another good choice might be Michael Elgin, as he's a pretty fresh face and this far into the year he should be popular enough as a challenger if not a champion.
Moving past KoPW is Power Struggle, and you can throw in a final challenger from the Climax if you want here or have Naito select his own opponent or even go a little crazy and make it a Los Ingobernales themed show with Naito's own stipulations for matches and shit. It'd be zany and not something Gedo would normally do but if the Los Ingobernales hype train goes that far then who knows.
After that you've got World Tag League, so you can put two LI teams in the mix across the two blocks and just start teasing new opponents for 2017.