All mail clients suck. This one just sucks less.

make_maildir.py

import mailbox
import random
import os

# sample messages from my mail archive
sample_maildir = mailbox.Maildir('~/MailDir/private/archive')
sample_messages = sample_maildir.values()

# create a new maildir with two mailboxes
os.mkdir("./TestMaildir")
box1 = mailbox.Maildir('./TestMaildir/box1')
box2 = mailbox.Maildir('./TestMaildir/box2')

# populate the mailboxes with sample data
for _ in range(100000):
  box1.add(random.choice(sample_messages))
  box2.add(random.choice(sample_messages))

muttrc

set folder = ~/TestMaildir;

# cache makes a huge difference, ~30s to ~5s to open a mailbox
set header_cache = "mutt_header_cache"
set message_cachedir = "mutt_header_cache"

set spoolfile = "+box1"

# date is quick, sort by "threads" adds 5-10s after mailbox load 
set sort = date
set sort_aux = reverse-last-date-received

# the default for change mailboxes is 1s, I have no idea why.
set sleep_time=0

# two mail boxes
mailboxes +box1 \
          +box2 \

# sidebar stuff, because I don't actually know how to use mutt with out.
set sidebar_visible = yes
set sidebar_width = 30 # width of sidebar
set sidebar_delim = '|' # sidebar delimiter
bind index,pager <down>   sidebar-next
bind index,pager <up>     sidebar-prev
bind index,pager <right>  sidebar-open