Updating my list
I am silly and forgot a big one, Dragon Quest!
And one kind of big one, Soul Blazer.
In addition, my ordering was a bit weird. I didn't put enough thought into it. While Xenogears is my favourite game of all time, there are no other Xeno games I can put in my top 10, even though all of the Xeno games make my top 50. I don't think I have gone a single season of any year since about 1988 or so where I have not played a core Mario game, or one of its many spinoffs. I can't even say the same about the Xeno franchise which began in 1998 - and currently amounts to only 6 games - against the, maybe, 50 Mario games I own. With multiple series of games and spinoffs that I love: Mario Galaxy, Mario Bros, Mario Kart, Super Paper Mario, Mario RPG, Yoshi, Dr. Mario, Mario Party, etc... no other franchise is so heavily represented in my library, so Mario is a clear number 1.
I am mostly going by the number of games I enjoy in the franchise, and the amount of time I put into games; franchises like Pokemon, Shin Megami Tensei, Disgaea, and others, require lots of time to get the most out of the games, but I find with all of those I have a tolerance of no more than about 35-40 hours, and then I feel like I am wasting my life. Xeno, Dragon Quest, Zelda, Harvest Moon, and Paradox grand strategy games are the only franchises I have put 100+ hours into one playthrough... and with those, I always considered high quality gaming time. Breath of the Wild is my first 100+ hour Zelda, I have played them all (minus the licensed out games).
I would love to put Resident Evil, Castlevania, Breath of Fire, Suikoden, and others, but each has issues. Resident Evil, I only really liked 1-3, and only liked 4 because of the Wii controls, I don't enjoy it at all without IR aiming. Castlevania, I was a big fan of all the games from the beginning, but especially Castlevania 3, Super Castlevania, Rondo of Blood, Symphony of the Night, and Circle of the Moon; I did not enjoy any post-Circle of the Moon, each game afterwards felt like it was falling more and more behind gaming trends, and they lacked the spirit of earlier games. Suikoden, I feel the same as Resident Evil, while I love 1 and 2, the remainder of the games felt a little weak to me. Breath of Fire and Lufia, games like that, I have always enjoyed, but have found every game in those franchises tend to have too many imperfections. Lunar, Earthbound, and others are like Suikoden, too few games I enjoy. Soul Blazer is just a trilogy, but I replay all of those games to this day, and would put all three games in my top 20 of all time, only bonus points for tacking on related games like ActRaiser.
Unfortunately, I have to say goodbye to Animal Crossing and Ace Attorney on my list; they got pushed off.
2. Xeno (gears, saga, and blade)
3. Dragon Quest
5. Final Fantasy (only 1, 3-8, Tactics, X, and the gameboy games that are technically other franchises)
6. Soul Blazer (Soul Blazer, Illusion of Time, Terranigma)
7. Paradox grand strategy games
8. Harvest Moon (now Story of Seasons and Rune Factory, screw Natsume's current "Harvest Moon" games)
9. Fire Emblem