It took me forever, and this is late, but these are the Pokemon I can picture each Fire Emblem lord starting with:
Marth gets Pikachu
Alm gets Bulbasaur
Celica gets Fennekin
Sigurd gets Piplup
Seliph gets Squirtle
Leif gets Mudkip
Roy gets Cyndaquil
Eliwood gets Charmander
Lyn gets Treecko
Hector gets Chespin
Eirika gets Chikorita
Ephraim gets Totodile
Ike gets Torchic
Micaiah gets Eevee
Sothe gets Froakie
Chrom gets Chimchar
Lucina gets Turtwig
I have a reason for some of them (just look at Treecko's final form, Sceptile, it looks perfect for Lyn, Eliwood & Charmander for obvious reasons, and Marth & Pikachu both being the mascots of their series, for example), but the rest I can just picture in my head working very well.