I think some of you guys are missing the point about all this - there really isn't much Iwata could have done - really - he had the option of turning the company into a F2P/mobile company four years ago and embracing that business model like many Japanese publishers did - or to take a risk and try to stay in the packaged software business and spending tremendous resources scaling Nintendo's capabilities to meet the bar of high-end software development without overextending themselves.
At that time people were questioning whether Sony was going to make a new console as the company was nearly bankrupt (and still is almost bankrupt - it's basically a zombie firm with a ridiculous amount of debt), and Microsoft had pretty much abandoned Japan (the source of 30% of Nintendo's gross profits). It isn't as if Nintendo could even have gone third-party - the only real options were to embrace the iPad and iPhone which were nascent platforms in Japan and had a style of games that Nintendo had never made.
If somehow Iwata were removed - the company would most likely move towards mobile and most likely free to play models since Iwata and his executive team are the last holdouts in the entire Japanese video game industry keeping traditional complete games a priority. I mean I guess some of you would want that because you want more free to play games, but I'm guessing a lot of you wouldn't be too happy about that. A new CEO would likely kill off Monolith Soft since they have been a perpetual cost center for Nintendo over the years, and probably cut off the dozen or so companies that Nintendo works with and keeps feeding like Grezzo, etc. I'd imagine they would kill Bayonetta 2 (or send it to die with zero marketing to cut their losses) and probably kill niche series like Pikmin from ever being produced ever again. Platinum in its current form would probably disappear since Nintendo has been effectively paying their bills over the past two years. MGR:R barely made them any money - they were hired as contractors - and a sequel to that game isn't going to be enough to keep everyone at Platinum employed. Nintendo's overall hiring plans would probably be frozen, and staff would be cut - probably at the high-end developers like EAD Tokyo which over hired to stock pile human resources for HD development over the past two years. Under a hypothetical new CEO, I wouldn't expect much in the way of new AAA console games from Nintendo if Iwata were fired since he is one of the few people who still believes in making them.
Shareholders aren't going to replace Iwata with someone that is going to make hardcore AAA IPs as a first party or as a third party for PS/Xbox platforms, or have Nintendo build a competitor to those platforms. The failure of the Wii U and the failure of their packaged software business in general (consider that out of 40+ million 3DS consoles - Zelda sold peanuts during the Holiday season) is going to lead investors to focus on someone that is going to embrace contemporary trends in gaming. That means lots of F2P an P2W and other things like low development costs on mobile to maximize gross profits. This has implications for the entire industry.
A world where Nintendo gives up on premium software is a scary one because it is going to drive expectations of all customers and spill across the entire industry. EA might be able to ride out the next few years with cheap updates to Madden and FIFA licenses and force yearly upgrades - Activision might have World of Warcraft money - which while declining rapidly - still keeps the lights on. But the former is effectively a peasant of Microsoft (and praying to be bought out by Microsoft or Disney), and the latter is deep in debt and is banking on a single game (Destiny) to deliver any profitability next fiscal year while depending on its Chinese investors to provide cash if they need it. Who knows maybe Destiny does great - but the millions it will sell to a core userbase aren't going to be enough to help Sony/MS drive their user bases up to 70-80 million needed to really achieve profitability at-scale.
Beyond that, Ubi's Just Dance money isn't going to sustain itself and Assassin's Creed is a franchise-in-decline. If Watchdogs fails to sell ridiculous numbers, I would expect Ubi to fully embrace F2P and focus heavily on mobile going forward. I can see them running to Apple and offering to make Rayman an iPad exclusive in return for cash payments. Take Two is already contracting its portfolio, and now it's more or less a two-products a year company. Bioshock4 and GTA6 might just be persistent online worlds with monthly subscriptions or a F2P model. I have a feeling NBA2K is going to go the F2P route in a few years as well - because that's probably where EA is going to take NBA Live to try and compete - and unlike the NFL - the NBA is probably not going to cut an exclusive with Take Two to preserve pricing power and risk lawsuits.
Even people like Peter Moore who have mastered the art of selling out their current employer for their next job and want nothing more than to see Nintendo suffer, are most likely trembling at hearing about Nintendo's current-year numbers.
I'm pretty pessimistic about the future of games, but even I can't accept this frankly dystopian vision of the future. I'll address the bolded points.
1. There was plenty that Iwata could have done, quite obviously. In another world, there is a Nintendo that came up with a better idea than Wii U, gave it a better name, launched with better flagship software than Nintendoland and came in at a better price point. That's just to begin with. In that better world their home console is not cratering the way it is now. Maybe it's not a huge success, but the Wii U is a function of terrible decisions piled on top of each other as much as anything else.
2. Of course Nintendo could go third party. The transition to PS4 development would be massively easier for them than the transition to phone/tablet gaming. One is an entirely new paradigm of gaming that as you point out does not suit most of their franchises. The other is just learning a new architecture, licensing an engine and making higher quality assets. There are 160m PS3s + 360s out there. There will be plenty of next-gen consoles sold. They could easily go, or could have gone, third party. I believe they probably one day will.
3. I don't think that there's any guarantee whatsoever that the new CEO forces Nintendo into mobile gaming. Shareholders aren't stupid - they must see that
a) It doesn't suit Nintendo's catalogue
b) They don't have the skill / expertise in that area, and it would take two years minimum to acquire,
c) You can still profit making software for PS3/4 and the Xboxes
d) You can still profit making handhelds if you don't have a home console albatross weighing you down
e) The mobile market is disastrously over saturated and very few companies are making money. You're throwing the dice as a new entrant to that market. You're also destroying the dollar value of your software forever once you start selling it for 5 bucks or less.
I'm not saying it won't happen. I'm just saying that painting that as the inevitable consequence of a new CEO is ridiculous.