For SFC2 I mostly use TMP and TOS, because SFC3 has TNG covered so well.
My spec file is a bit wierd, but I think they're valid based on the specs of certain ships.
I'll do just my Fed stuff, because that's where most of my modifications have taken place.
I use all upgraded in-game ship models and quite a few others.
My entire CA section belongs solely to the Constitution Class. The CA is Aduril's Cage Enterprise and the CC is Stress Puppy's series Connie. The CA lineage follows the Phase II developement, with the CAR, CA+, and CAI models being Ghost's, Stress Puppy's, and Moonraker's Phase II varient constitutions respectivly (It's odd, that the models actually seem advancements to eachother. Ghost's retains a very TOS look, while Moonrakers looks late TMP) The CC+ and CB are P81's connie with Wil's 1701 repaint and p81's 1701-A registries respectively.
My CAD and CADR models follow the Decatur/Belknap line. The CAD+ is Moonrakers Heavy Drone Cruiser.
My NCLs are all Miranda's or their variants. My NCL, NCT, and NCT+ are all Stresspuppy's TOS Miranda while the others are Moonraker's TMP Reliant.
My NCA is Monraker's Constellation.
My BC section is made up of Moonraker's various Excelsiors, including the NX Excelsior for the BCG and the Ent-B for my BCJ.
MY FF and FFG are P81's Daedalus and Cleeve's Discovery pre-TOS ships.
My Dreadnaughts are all Moonraker's Ulysses except for the DN and DN+, which are StressPuppy's Star Empire and Moonraker's Dominion.
Aside from the listed incedents, each other ship class has it's own model. Usually, the + or R version is a TMP or Phase II model depending on how many upgrades of the design there are. Is a TOS version of a ship does not exist, such with the Oberth (my FFB) then I'll stick another model in the basic ship's slot and disconnect the upgrade capability.
Other modifications that I've made in general is to increase the quality while decreasing the quantity of Fed weapons. For instance, all the TOS ships lighter than a Dreadnaught have 2 Phaser 4s mounted on the saucer with an FX firing arc and NO other phaser weapons. During the entirity of TOS, I saw the Enterprise use only those heavy phasers mounted on the saucer underside. I'm guessing that this single phaser mount is turreted with a 270 degree firing arc. The DN has 2 Phaser 3s on either side of the saucer and on the engineering section covering the right, left, or stern quarters depending on placement. Forthis reason, I use the TOS Phaser sound for the Ph4. Usually, each TOS ship has just 2 torpedo tubes, except in the case of the CC, which has 3, and the DN, which maintains all 4. All TOS ships have had their maneuverability decreased by one degree. All TMP Fed specs have been left unchanged for the most part. However, I have removed missiles from all Fed ships save for the Drone cruisers and Guided Missile Destroyers and Frigates.
I've also given the Klinks photon torpedoes where appropriate, namely to the later model D6 and D7, plus the Birds-of-Prey. They've been given cloaking power where appropriate also.
Between SFC2 and 3, I'd have to go with 2 for right now because 3 isn't perfect yet. But 2 is great for TOS/TMP adventures while 3 can cover TNG. I'f I could find enough models, I'd have SFC1 cover TOS entirely and 2 cover just TMP, but there aren't enough TOS models for SFC1 to turn that trick.