In retrospect the warning signs with Vettel were there when he was demolished by Ricciardo in 2014. Much like they were there when Alonso nearly went off the rails towards the end of the 2006 season.
I've said it before and I'll say it again, Vettel wasn't demolished by Ricciardo. The stats say he was, but in two of the races Ricciardo won, Vettel was ahead, with a team strategy mistake costing him one victory and a safety car coming out immediately after he'd passed pit entry the other. That one was particularly harsh as Ricciardo was miles behind him at the time, but was the first able to pit and he duly took the lead when the drivers ahead of him pitted the next lap.
I'm not sure anyone expected Ricciardo to take the fight to Vettel, but that was as much about the 2014 regulation changes as anything in my opinion. Vettel was unmatched in the exhaust-blown diffuser era - no other driver had the confidence Vettel had and it was a sight to behold, despite us all hoping his relative dominance would be challenged more often. Even his own teammate and championship rival stated "I can't do that", something a teammate never says. I don't think Ricciardo would have been anywhere near as strong in 2014 if the regulations had stayed the same.
Vettel's never looked at home in the hybrid era, and you could visibly see the pressure on him at Ferrari. I think he'll be relieved to step away in the long-run.
As for 2006, Alonso's title was won despite the FIA and Ferrari's overly close relationship (everyone remembers how close they were in the early 2000s; far more so than any perceived issues now). First with banning the mass damper mid-season, despite scrutineers saying it was legal and even with the FIA agreeing to it as it was developed - in the end FIA were appealing the decision of their own scrutineers! The second being one of the most ludicrous stewarding decisions I've ever seen, when Alonso was being penalised for driving flat out and being something like 5 seconds ahead of Massa in qualifying at Monza - something Ferrari claimed held up Massa, yet last year's qualifying showed exactly the opposite through everyone's desperation to get even a sniff of a slipstream.
I'm not sure quite where Alonso is supposed to have gone off the rails in 2006, towards the end or otherwise. Schumacher made more mistakes than Alonso over the season, crashing in races in Melbourne, twice in Hungary and again in his final race in Brazil. I don't recall Alonso making any serious mistakes all season - indeed it was probably one of the best campaigns in recent-ish years.