I like all the theories put forth
My current operating theory:
1. The Enterprise looked like the diagram seen in "The Enterprise Incident" before or during the early part of Pike's command.
2. Enterprise receives a slight redesign and refit, losing the lower beveled saucer edge and the warp nacelles are moved closer together. She may have also been enlarged as well.
3. When Pike turned over command to Kirk, the Enterprise underwent a minor refit and upgraded systems including the turbolift location on the bridge. Crew may or may not have been bumped up to 400 at this point as Mitchell says there are at least 100 women on board. The ship may have also been *specially outfitted* for going out of the galaxy for a period of time. The ship might also instead of being bumped up to 400, might have been an even ratio of men and women for the extra-galactic mission.
4. When returning from the galactic barrier, Starfleet shelved the extra-galactic mission and refitted the Enterprise for normal exploration within the galaxy. The turbolift location in the bridge is once again moved.
5. After the events of "Balance of Terror", Kirk has photon torpedo launchers added to the Enterprise as a secondary weapon.
6. At some point, the Enterprise's energizers are upgraded to handle dilithium crystals.
7. The computer system gets an upgrade during general repair and maintenace at Cygnet-14. After "Tomorrow is Yesterday", Enterprise puts in for a 3 week overhaul at a Starbase to undo the changes.
8. Between Season 1 and 2, the Enterprise receives an engineering upgrade, moving the energizers to the newly expanded engine room.
9. The engine room and engines are upgraded over S2 and S3 (and presumably the remainder of her 5 year mission)
10. Enterprise completes her 5 year mission and undergoes a significant redesign and refit for duty over 2.5 years in "The Motion Picture". Overall size is enlarged with majority of the ship built new from the ground up.
11. Enterprise is refit and modified by "The Wrath of Khan". Direct access to the dilithium/energizer is added as well as an extra ladder in the engine room. Other cosmetic changes are done to the bridge.
12. Enterprise is destroyed in "The Search for Spock"
13. Enterprise-A is commissioned under Kirk's command in "The Voyage Home". Different bridge design and turbolift locations.
14. Enterprise-A engine room is modified/upgraded by "The Undiscovered Country". The TNG-like warp shaft replaces the old shaft and a transparent booth/control area is added. The turbolifts are once again moved on the bridge.
15. Enterprise-A retired after Kirk takes a very very long side trip via some "star to the right" before returning to Earth