When you close the lid on an Apple laptop it first goes into a suspend to RAM state Apple calls "Sleep mode". You can tell it's in this mode because you'll have a slowly pulsing white light visible on the front face of the system.
In this state, the system is effectively turned off, except for the RAM which is kept active, and some circuitry needed to power the system back up.
Now, if your battery gets to critical levels during this time, it will go into what Apple calls "Safe sleep" IIRC, and everyone else calls Hibernate. It will dump the contents of RAM to disk, and shut the system off completely.
For better or worse, there is no way to dictate that the system should go into safe sleep when you close the lid, not merely sleep. So if you know you're not going to be using the system for a couple of days, just shut it off. Having to wait 30-90 seconds for the system to boot back up about once a week is not that big of a hardship. Start the thing booting, go get some coffee or something, and by the time you get back, it'll probably be ready.
And when you think about it... When the system is running you get maybe 4-8 hours worth of battery life. In sleep mode you're getting over a 48 hours. Sounds like pretty good battery life to me. Nothing at all seems wrong here, except your expectations.
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