I'm opposed to Iwata stepping down. I understand that the Wii U is currently failing and I understand that third-parties don't want to make games for Wii U, but neither of these things affect me personally. I have a Wii U and I really like what it has provided so far. I honestly don't care whether or not anyone else in the world buys the system, because I have one and I enjoy it, and I definitely don't care whether or not it has third-party support, because I buy Nintendo's systems for Nintendo's games. Sure, it'd be nice if Nintendo found a way to get more Wii U's sold, as this would enable them to keep making awesome games for a longer time. In the end, though, I'm not sure replacing the management would even change anything; not without changing the entire company, anyway.
Nintendo's current issue is their image. The reason people aren't buying Wii U isn't because they genuinely think it's a bad system. It's because of the abundance of ignoramuses in the gaming community with the mentality that all Nintendo does anymore is 'rehash' their games (use of this buzzword is essential), which are only made for twelve-year-olds and moms anyway, and that somehow lack of third-party support and lack of online functionality in every single game are bad things. Iwata has literally nothing to do with these delusions, and it would take a lot more than swapping him out to eradicate them. Whether or not these problems even are problems is moot.
Take lack of third-party support for example. Setting aside the fact that most third-party games pale in comparison to Nintendo's games in terms of quality, the presence of third-parties on Wii U would make no difference. Nintendo has had plenty of third-party support in the past. Gamecube had plenty of it and it's their worst selling console to date (aside from Wii U, which is still very young). Wii had plenty of it--in fact, the vast majority of content on Wii was third-party; 'shovelware' as they call it--and while the console sold tremendously, most of the console sales probably came from the motion controls gimmick and Wii Fit, a first-party game, and everybody else bought Smash Bros. and Mario Kart and New Super Mario Bros. Wii and not a single thing else. Evidently, there's no reason to believe that bringing third-parties over to Wii U would solve anything, and this definitely isn't a 'problem' which could be attributed to Iwata anyway. And this is just one example.
Let's say that the management at Nintendo does receive an overhaul, though. They put someone with hip, fresh ideas in charge and they get that third-party support and incorporate that online and everything. What would set Nintendo apart then? What could Nintendo possibly do, then, that Sony and Microsoft aren't already doing better? "Mario and Zelda!" you shout. Psh, no one wants those dumb rehashes anymore. I'm not twelve or a grandma; I need the dark, gritty games that all of my mature friends and the Let's Players on YouTube are playing. Titanfall, Battlefield 4, etc. "Okay, I'm sure Nintendo is more than capable of making their games appeal to those people." Oh, so abandon their current audience and potentially start entirely from scratch. That'd be a good plan?
If Nintendo were to change their focus to try to capture the people buying PS4's and Xbox One's, it'd be a waste of time and money, because those people already have a home. Nintendo needs to keep being unique in order to survive in the industry. Changing to match the competition, be it at the management level or otherwise, would only get them crushed
These are only my thoughts, though, and I'm no industry specialist. As it stands, I like the system and I like its games. That should be reason enough for me to prefer things at Nintendo stay the way they are.