If I remember correctly, he said that it was the best franchise. I don't think he mentioned any one Fire Emblem in particular. It'd be kinda difficult to compare a series to a single game (so far).
Anyhow, I prefer Valkyria Chronicles to any single Fire Emblem game. Although I pretty much love everything about Fire Emblem (except the odd bit of cheesy dialogue), I prefer the battle system in Valkyria Chronicles. I found it to be much more fun.
As a series, I'd go with Disgaea. It's fairly basic in terms of gameplay but it has countless hours of playability, customization and just oozes both in charm and hilarity. You can get both the first two on the PSP and the first one on the DS, I believe. My favourite in the series would have to be the first, followed by the third.
As for my favourite SRPG it'd either be Valkyria Chronicles or Final Fantasy Tactics: The War of the Lions
