They have limited server tech.
The more information you have loaded up when you play, the more time it takes for the backup save to happen (to avoid long time interval rollbacks on server crashes)

The more data they have to save per character, the more time it takes, that's the reasoning they gave.
Retainers are a different business, since they're accessed much more rarely and by far far less players at a time compared to personal inventories that undergo constant change during play (getting items, switching classes, etc)

They're working on improving the process as far as Yoshida said, but I'm not sure when or if it will translate into more inventory space down the line. Fingers crossed.