Should I design with "N" parts or newer parts?
The 2Nxxxxx designation was a industry wide designation that was derived by the organization that became the EIA.  While different manufacturers had their own 2N number, with others second sourcing some parts, they maintained a common naming scheme for these parts across the industry.

The concept of obsolescence for discreet parts doesn't fit.  Yes, certain parts will have superior Hfe (for example) or handle higher current (as another example), but a part is the right part if the specifications fit your needs (performance, cost etc.) regardless of it's history, age or process technology.  The only real measure of obsolescence is whether or not you can buy the parts to support manufacturing.

On Edit: The standard is Jedec 370B - which was a RETMA (Radio Electron Televsion manufacturers Assoc.) -> EIA -> JEDEC standard based upon the old tube/valve designators from the RMA (Radio Manf. Associations).  N designates crystal rectifier.

Standard is downloadable here as JESD370B.