I don't have the time this week to do it, so I'll just list them, sorry.
I'll do 5 from each (though I haven't played many FF games), but overall I'd put FE and Fate characters over FF, having a tie between the first 7-10 of FE and Fate overall (it'd go like "tie between 1st and 1st, then tie between 2nd and 2nd, etc.").
Top 5 FF: Luneth, Aerith, Cloud, Terra and Tifa. Not much original lol, but I haven't played many.
Top 6 FE: Catherine (3 Houses), Reinhardt (Thracia 776), Dorothea (3H), Marianne (3H), Leonie (3H) and Chrom (FE Awakening).
I have to say that in my top 20 I have from mostly every game, not just from recent ones like 3 Houses (I have some like Raven from BlazingB, Selena from SS, Milady, Idunn, Igrene and Thea from BindingB, Ike and Mist from PoR/RD, etc.)
Top 5 Fate: Quetzalcoatl, Cú Chulainn, Sasaki Kojirou, Medea and Mordred.
*Top 11 Type-Moon: Ryougi Shiki, Quetzalcoatl, Aozaki Touko, Cú Chulainn, Sasaki Kojirou, Medea, Mordred, Caenis, Enkidu, Gilgamesh and Mitsuzuri Ayako.
