I'm thinking if the server dies, MyISAM tables tend to corrupt more easily, and repairing a table that large will take a long time.
But that's the only thing I can think of -- and the speed/size of MyISAM tables have a lot going for them, I'd be tempted to go with MyISAM. Anybody else?
Ya, recovery time is a big deal. It's like the difference between ext2 and ext3. With ext2 a crash is gonna require a lengthy and painful fsck, especially if your table/filesystem is large. A journaled filesystem is a lot like a database engine with transaction/redo logs. After you crash, you replay the last 'n' uncommitted transactions (they're all idempotent so you can do this multiple times) in the journal and you're good to go.
Also don't forget about MyISAM's lack of row level locks, and really nowadays there are fewer and fewer cases where it's faster than InnoDB.
But that's the only thing I can think of -- and the speed/size of MyISAM tables have a lot going for them, I'd be tempted to go with MyISAM. Anybody else?