I would like to see the Devs allow a broader range of registry numbers, say, make the minimum allowable something in the range of 10000 or 10999. I would like to use the registry used by my real life fan club chapter, USS LoPresto NCC-29665-C, but alas, the numbering scheme is locked at 99000 and above.
Like it or not, CBS are allowed to protect their IP from being used in untoward ways. I'd say keep the registry system as is, with maybe some level of expansion up to around 999,999 (if it's not that already, I'm not complaining about it as it is.)
The article you linked clearly states that there's no real pattern to the registry numbers.
"Summarizing, as a matter of fact the known registries of Starfleet vessels may only roughly correspond with the ages of the ships. None of the various theories accounts for all of the inconsistencies, so it should be tolerated that ships are sometimes arbitrarily numbered."