For those unfamiliar with Tencent, they are a massive, publicly-traded conglomerate out of Shenzhen, China, with holdings in tons of tech-related industries. With regards to gaming, they are majority owners of Riot Games (League of Legends) and Supercell (Clash of Clans), and own stakes in Activision Blizzard, Epic, Ubisoft, Paradox, and several other smaller game companies.
There's a lot not said in the announcement, which is not surprising given the fact that it's a brand-new concept today. However, based on what we know right now, I think we can safely make a couple of assumptions. First, it doesn't seem like this will change too much in Square Enix' core business. Flagship franchises currently managed by the main Squenix offices will likely remain the same, since the new company is exactly that - new and separate. Second, this will likely impact Asian markets first, given the fact that the new partnership is between a Japanese and a Chinese company (no word yet on where the new company will be headquartered). Third, there's a pretty good chance that there might be some bizarre concepts using Final Fantasy characters and settings showing up in the future.
Source: Siliconera, Wikipedia