Were I to do this my content would be late 20th century to TMP era (including TAS since it's essentially the TOS era).
Since FJ did show us things that were never seen onscreen one could build on that to a limited extent in that I would include some things as long as they were consistent with what we saw. Of the new ship classes he showed us I really didn't care for the transport/tug or the dreadnought. I'd drop the FJ transport/tug and show one similar to what Masao
has on his Starfleet Museum
site in addition to showing the freighters seen in TAS. I'd drop the dreadnought and show a Surya
type frigate instead.
I would include a limited number of pre TOS era ships to give something of an overall feel for those eras without trying to fill in every blank. Ditoo with alien vessels such as early Romulan and Klingon ships.
I will say right out that if I were doing this (and I conceivably might) I would be totally ignoring things seen and ENT and FC. I just think they really dropped the ball on those. The only thing I ever saw in ENT I liked were their Romulan Warbirds and only because they actually looked TMP era rather than pre TOS. Masao
has done a much better job in regard to 22nd century Romulan ship designs.