Anyone knows a drama where the female lead is ugly/otaku/tomboy and have low self esteem? But without she changing into pretty or such. Ah, BL is okay too, but the bottom one is the one that has low self esteem. Thank you!!! 

You can check these.
Busu no Hitomi ni Koishiteru (2006)
Busu no Hitomi ni Koishiteru (2019) Remake

This might fit too. I haven't watched the movie but as much as I can remember, the FL is very timid but not otaku/tomboy or ugly.
From Me to You (2010)

If you don't mind older drama
Nobuta wo Produce (not pretty + social awkward + low self esteem)

Recent years drama
Todome no Kiss (low self esteem + social awkward)
Dakara Watashi wa Oshimashita (low self esteem)

Today's Kira-kun -FL has low self esteem, therefor growing out her bangs to hide her face. She is also shy and doesn't interact with others often. 

An oldie but sorta-goodie from 1996: Hitonatsu no Proposal.