A grown ups Intrepid Class ship. Old school saucers shapes are so.... 
(Prometheus Class is pretty cool too)
Class 9 warp drive.
Bio neural gel packs.
Warp core ejection capabilities.
Landing capabilties.
EMH.
Ship board holodecks.
Borg enhanced astrometrics.
Delta Flyer.
Mobile Emitter.
Not sure whether to include the replicators but they are something that needs to stay. I can't remember when they first surfaced. Also there are certain basics Star Trek needs to have. Transporters/Energizers. Later versions are better though than using the flip phone type from TOS.

(Prometheus Class is pretty cool too)
Class 9 warp drive.
Bio neural gel packs.
Warp core ejection capabilities.
Landing capabilties.
EMH.
Ship board holodecks.
Borg enhanced astrometrics.
Delta Flyer.
Mobile Emitter.
Not sure whether to include the replicators but they are something that needs to stay. I can't remember when they first surfaced. Also there are certain basics Star Trek needs to have. Transporters/Energizers. Later versions are better though than using the flip phone type from TOS.