That's only because people look at the roster for representation.
Let's look at how the Pokemon and FE franchises are represented on the Wii U version.
Both get 6 characters, yes. But all of Pokemon's are unique while FE basically has three Marths. That means half of its roster has the same fighting style, which might be a reason why people complain about too much FE. Heck, even Corrin almost looked like a Marth clone until we were shown that they'd use their dragon abilities more than they do in their own game.
Just for trophies, Pokemon alone has 106 trophies out of the total of 743 (incuding DLC). How many does FE have? 23.
Both have two stages, one from Brawl and one brand new. But for the brand new ones FE's Coliseum is just a generic walk-off stage with alternating platform layout while Kalos Pokemon League looks absolutely gorgeous, has different layouts which also grant different hazards and a ton of Pokemon cameos.
When it comes to items, FE only gets a Lyn Assist Trophy while Pokemon has not one, but
two items; Poke Ball and Master Ball. They allow you to summon one Pokemon out of a list of
forty.
Music-wise, Pokemon gets 24 songs. FE gets 23, two of them being Lost in Thoughts All Alone, which were added alongside Corrin.
tl;dr FE does have a lot of characters, but said characters, the music and the Lyn AT is the only representation the franchise really gets. The main problem is how 2 of them are Marth clones (Roy, Lucina), meaning half of its roster is more or less similar.