I'm probably gonna get some flack for this, but I'd say Mario and Luigi RPG. The series is very charming and the battle system is very fun and unique.

Also, I loved Xenoblade and it's one of my favorite standalone RPG series of all time, but I haven't played X to count that series as my favorite.

Classic FF is pretty great too.

Elder scrolls for me

Dragon Quest

Discounting all IPs with less then 3 games, but still tough one for me to choose:

I love Fallout 1/2, I think 3 is between meh and decent, NV is between decent and fine, but 4 is just horrible, and I pretty much expect them to get even worse.

I love Gothic (yes, even 3rd) but there's only 3 of them...this can change in the future, but until then...

...I'd have to go with Might and Magic, since there are 9 of them (well, 10 if we count Legacy), sure, some of them are pretty bad, but there is both quantity and quality in that franchise.

I have a few, but Fire Emblem is probably my favorite.

Borderlands of course

Rightnow it's Xenoblade, then it's fire emblem & dragon quest

My favourite by far was Suikoden, next in line are Lunar, Dragon Quest and Fire Emblem. The only new franchise I liked from last gen was Valkyria Chronicles, Lost Odyssey and Resonance of Fate could join it if they ever get a new entry.

Fantasía Final.

Hmm... Witcher probably... Golden Sun and Mass Effect come to mind too.