My opinion on ships to use. First I am assuming no actual shuttle or similar ships, Runabout, Delta Flyer, even Starfleet 2 man attack ship/ Maquis Raider aren't technically shuttles.
TNG and TOS and Original films were limited by Model construction, so pretty much any original model that has real promise would get picked, as compared to later DS9, Voyager, or Enterprise, where ships were created for almost all races we were shown.
Also for myself this is Trek based on materials that would have been part of the art department and approved by executive producers (film and tv), not things like FASA (Loved them as a kid), not the old technical Manual, not novels and computer games.
TNG produced many cobbled together models from spare parts, redressed many models with minor differences, and even created some out of plastic and razors, which I also won't consider as in my mind they aren't serious work.
TOS
1. Original Enterprise (Will be done)
2. Romulan Bird of Prey
3. Klingon D7
4. SS Botany Bay
5. K7 Station
6. Fesarius (once mentioned and then later said not likely)
Those are the only TOS pieces that I could see making any cut due to lack of detail on others (like the Tholian ship of that time). But I would still get it.
TOS films
7. Enterprise Refit (Done and poorly)
8. Klingon Ktinga (Done)
9. Enterprise A (to be done)
10. Regula One (yes its a redress put upside down, but it is the more prominent station)
11. Reliant (Done)
12. Excelsior (Done)
13. Oberth (will be done)
14. Klingon Bird of Prey (Done)
15. Space Dock
16. Mechantman (first used here and had several later uses and redresses)
TNG
17. Enterprise D (done)
18. Ferengi Marauder (done)
19. Romulan Warbird (Done)
20. Borg Cube (Not stupid Lamp)
21. Stargazer (Done)
22. Cardassian Galor Class (Done)
23. Nebula Class Variant (kit bash and a good one) - Thank God not the Phoenix (Done)
24. Klingon Vor'Cha Class (Done)
25. Romulan Scout Ship (Not the redressed Science Ship)
26. Enterprise C (To Be Done)
27. Tamarian Cruiser (also used as T'Lani Cruiser, and a redress for others)
28. Pirate Ship Destroyed in Unification (Seriously could lose this one)
29. Borg Ship from Descent (mentioned)
30. USS Pasteur - I really, really want this one.
31. Future Enterprise D ugly 3 nacelle kitbash (Done)
TNG has a few others of course Jonalin, reused ship in Gambit I and 2 from DS9 first season), and the Pakleds ship that was used in TNG more then once, DS9 and heck even ENT.
TNG Film
32. Enterprise E (Done)
33. Borg Sphere (done)
34. Enterprise B - ugly modification of original Excelsior model (Will be done)
35. Akira Class (Done)
36. Steamrunner Class
37. Norway Class
38. The Phoenix
39. Saber Class
40. Son'a attack Ship
41. Federation Scout Ship
42. Ru'afo Ship (really didn't care for any of the Son'a but they played a major role in a film)
43. Romulan Valdore (Will be Done)
44. Shinzon's transforming Reman ship (I hate ships that transform)
TNG films leaves still several other options. The ships Guinan's people were on, The Stellar Observatory, Captain's Yacht, the Solar Collector, the Romulan/ Reman attack craft, the Holo ship.
DS9
45. Deep Space Nine (Done)
46. Runabout with Roll bar (actually would rather have one with out) (Will be done)
47. Bajoran Freighter (Redress of Paklads ship, but used several times for Bajor)
48. Bajoran Assault Vessel
49. Bajoran Impulse Craft (Kira and Dax used in Siege)
50. Maquis fighter (later used in TNG and Ds9 as Federation Attack ship)
51. Hideki Ship (Will be done)
52. Jem'Hadar attack ship (Will be done)
53. Solar Sailer (Done)
54. Negh'Var (Will be Done)
55. Karemma Ship (redressed for several others)
56. Defaint (Done)
57. Cardassian Freighter (also used as Klingon Freighter)
58. Ty'Gokor Station
59. Jem'Hadar Cruiser (Done)
60. USS Centaur (kitbash and a good one)
61. Jem'Hadar Battleship
62. Breen Cruiser
63. Xhosa cargo freighter (You might notice I like the various cargo ships used on Trek)
64. Dominion Station
65. Daedalus class ship
Ds9 had several other options, from a huge number of kit bashed ships to various alien crafts of the week. Wouldn't mind the orbital weapons platform either.
Voyager
66. Voyager (Done)
67. Maquis Raider (will be done)
68. Kazon Raider
69. Kazon Carrier (large Kazon/ Trabe Vessel)
70. Array
71. Vidian Ship (if they must) Vidians only had redressed ships if I recall, but they were a major early player for Voyager, and one of the better designed races.
72. Voth City Ship (wouldn't mind the Medical City Ship in Critical Care either)
73. Bio Ship
74. Kremin Time Ship (Done)
75. Hirogen Ship
76. Dauntless (Done)
77. Malon Freighter
78. Delta Flyer (Done)
79. Ship from Disease (Terrible episode great ship design) but would be tiny as hell (for a long time, the most detailed Cgi ship on Trek, go figure).
80. Borg Queen Diamond
81. Prometheus (Done)
82. Equinox (Done)
83. Raven
Voyager as a seeming less endless number of ships that could be used, some of really nice design, some utterly crap.
Ent
84. Enterprise (done)
85. Suliban Cell ship
86. Suliban Helix
87. Forunate (One of my all time favorite designs)
88. Intrepid class
89.Klingon Raptor
90. Klingon Bird of Prey (Will be done)
91. Klingon Freighter
92. Early Romulan Warbird (Done)
93. Romulan Scout (will be done)
94. Andorian Ship (Will be done)
95. Vulcan Surak Class (Will be done)
96. Vulcan D'Kyr (really want this one)
97. Orion Vessel
98. Reptellian Vessel
99. Xindi Insect vessel (Done)
100. Xindi Aquatic vessel
101. Degra's Vessel
102. Other Xindi Vessel (unknown which race).
103. Sphere or Xindi Weapon
104. Nx-Alpha
105. Horizon
Enterprise had a large number of ships built for it and in many ways they showed a large improvement over the alien of the week ships built for Voyager.
So thats basically my wish list trying to keep almost entirely to well known ships, or ships that played important roles in major story lines. Or ships that were seen many times over.
And that takes us way past 90 ships, doesn't hit the new JJ timeline (though I think most of those will fail under specials, unfortunately, generally love the films with the exception of how little distance is shown and the design of ships, the earth station is an exception as well as the shuttle, both of those I really enjoy).
So without digging up alien of the week ships (with a very few exceptions), without mining the vast number of kit bashes that TNG and DS9 and Voyager used both model and cgi versions), and without doing duplicates of any nature. The film and tv universe as plenty to use.
Now I am not totally against outside ships (theres a ringship I would love, Love to see), I want to see them really use the full line up of material actually created and designed by the various art departments that were hired for the show first.
