Some deserve being up there, some less. I didn't find Kimi no na wa bad, or FMA:B. Definitely not enough to call it trash lol, you guys trying to be edgy here or what is the particular dislike? Genuinely interested, not a FMA:B fanboy here.
Lets go through some of the top scorers on MAL though and my opinion on those:
#1 FMA:B - probably wouldn't put it in first place, rather #30-50
#2 Kimi no na wa - overrated, though not bad
#3 Gintama - slightly overrated. Granted I didn't watch many eps (12), I didn't dig the comedy too much
#4 Stein's gate - deserved
#6 Hunter x Hunter - matter of taste, but for me deserved. Definitely the best shounen fight anime.
#11 Koe no Katachi - I wouldn't put it this high, but it wasn't bad
#17 Code Geass - dunno, but this anime really clicked with me. I'd put it even higher.
#19 Made in Abyss - great first season, would maybe put it even higher. Depends on what is yet to come.
#22 Shigatsu wa Kimi no Uso - diabetes inducing romance, but I liked it. Liked the soundtrack a lot, deserved place.
#26 Cowboy Bebop - deserved.
#32 Boku no Hero Academia - deserved I guess. Maybe a bit lower.
#39 One Punch Man - deserved, would maybe put it higher than Boku no Hero Academia.
#40 Tengen Toppa Gurren Lagann - I'd rank it slightly lower.
#46 Monster - yikes, overrated garbage.
#48 Death Note - probably put it slightly higher than this, at least first season.
Honorable mentions:
#214 Redline - how is this not higher.
#235 Trigun - I'd put this one higher as well.
