You can save your messages in multiple formats for later reference. I dislike cleaning out my PMs and managing saved message files, but it's a small price to pay for everything this site provides. Storage for all these 1's and 0's costs money, and I'd rather that storage space get used for more public content than for larger individual PM boxes. At least we have the ability to save our PMs. My opinion is if my PMs are important to me, then I'll make the effort to back them up. My PMs are not important to the majority of members of this site.
It may be difficult to work out the payment scheme but perhaps the admin could make larger PM boxes a benefit of paid membership. That is if paid membership would offset the cost of more storage.
Of course all of the above is assuming the current PM system is not a product of software or host limitations. If the software or host offers the flexibility and time permits, then I imagine the admin will explore or has already considered user suggestions.