I think fans are more fickle with the whole console wars stuff than the companies themselves.
Cloud being in Smash had to be the result of a deal between Nintendo (publisher and copyright owner of the Smash Bros. series) and Square Enix (copyright owner of Cloud and the Final Fantasy series).
Did SquareSoft shift the development of Final Fantasy main titles since the N64/PS1 era? Sure, they did. They did it because they wanted to deliver a game that matched their vision for the game and the N64's specs didn't allow for it. Was it kinda stabbing in Nintendo's back? Sure, it was, but business is business.
As FF7 went to be a successful entry of the series, it makes sense that a lot of the PS crowd became the primary audience of the series' main titles.
Nowadays, Square Enix produces games for both Sony and Nintendo consoles. Some of Square Enix's important IPs are exclusive to Nintendo such as the Bravely series, which is pretty much classic FF in many ways and obviously caters to the FF fans that played the earlier titles on the NES and SNES.
Series such as Dragon Quest and Kingdom Hearts have presence on both Nintendo and Sony consoles.
There are also plenty of Final Fantasy spin-off titles and remakes/re-releases of the NES and SNES titles on Nintendo consoles, so it's not like the series left Nintendo consoles completely.
I'd say that Final Fantasy has as much ties with Nintendo as it does with Sony, though in different ways. Perhaps it can be argued that Cloud isn't the ideal character for a Nintendo-centric crossover and that another character, mainly from the NES/SNES titles, could've been picked instead. There are good choices such as Black Mage or Terra.
It's something I can agree on, but Cloud is possibly the most popular FF character, so him being chosen to represent the series as a whole isn't too far fetched, so it's a choice that has some merit in regards to standing next to characters such as Sonic, Pac-Man or Ryu.
Cloud, as an individual character, has about as much ties with Nintendo as Snake does, so they're both similar in that regard. However, there is one big difference between Cloud and Snake: the series Cloud comes from has far more ties with Nintendo than the MGS series does, so it can be argued Cloud has more merits to be in Smash than Snake does based on this principle.
To be honest, I think it's clear that Smash Bros. is more and more accepting of third party characters than before. I think it's a natural evolution for the series in order to keep it fresh and interesting. It's not just about Nintendo exclusively anymore, but also focusing a little bit on gaming as a whole. Of course, it is still going to be primarily Nintendo, as the grand majority of the content is still based on Nintendo franchises.
That makes sense: Smash Bros. is owned by Nintendo and it's always marketed and advertised as a Nintendo crossover. That's the primary draw of the series and something that will never change. I don't believe the series will be losing that focus anytime soon.
At 5 guest characters out of a 56-character roster, it's clear that third parties are still a minority. 5 out of 56 is 8.9% of the roster. It's not even a tenth of the total number of characters. Adding to that, there are only 5 third party series with content in Smash out of dozens Nintendo series.
Smash isn't losing its focus at all, but it is evolving, as every series does. The inclusion of third party characters is simply a part of that evolution. The Smash series still stays true to its roots all in all.