All of my records (3,000+) are in outer sleeves. After they are cleaned, I re-sleeve the record in a high quality inner sleeve. I like Grooveguard Archival inner sleeves, similar to what you get from Mofi. I store the record outside the outer sleeve and behind it for ease of access and to protect the outer sleeve. I like the Sleeve City Deluxe Oversized Ultimate 5 mil sleeves. They may take up a little more space, but aren't too snug and easily accommodate double albums.
I often leave the shrink wrap on the outer sleeve if it has hype stickers. While I recognize that sleeves with flaps are "better", I strongly dislike them, especially the ones that come with Japanese pressings with the sticky stuff on them.
If I see the shrink wrap starting to deteriorate on any of my records, or detect mold, I may change my ways, but I've yet to see that happen and will probably be dead before it becomes an issue.