First thing’s first…
The Empire had over 25,000 Imperial-class Star Destroyers, with appropriate numbers of other classes of ships. Around a dozen SSD’s, tens of thousands of cruisers, corvettes, frigates, gunboats, and millions of fighters. They outnumber the Federation more than 2-to-1 with just Star Destroyers, however. And that’s being VERY generous for Federation ship numbers.
Second thing…
Slow. Slow slow slow. SLOW. Go pop in First Contact again. Fast-foward to the end. Data fires a spread of quantum torpedoes at the Pheonix, from visual (read: less than 10 km) range. Torpedoes take about twenty seconds to traverse that distance.
That’s PITIFUL.
Even allowing for a bit of “embellishment” on the part of the FC effects guys, you’ve still got weapons that lose all advantage by their lack of velocity.
Anyway…
As I’ve said in the other thread, all of the Federation’s advantages (range, maneuverability) can be countered, relatively easily, by the Empire. However, the Federation can NOT counter the Empire’s vastly superior FTL speeds and sheer amount of firepower that they can deliver. It will only take a single encounter before the Empire realizes, “Hey… these guys shoot from far away.” The microjump - or multiple-jump - tactic that I described in the other thread would come into bear. The Federation crews just simply don’t have the reaction time to escape from an ISD appearing suddenly from hyperspace, guns blazing (there’s no way to tell that they’re coming). Even if the Fed crews manage to keep their bearings, it would take them a dozen seconds or so to whirl around, plot in a course, and jump to warp… and in that time, a hundred turbolaser blasts would pound against its shields. And since their shields seem to be relatively porous, some of that energy would bleed through to the fragile hull.
Given that Federation ships tend to explode after receiving only a tiny amount of damage (Cause and Effect), the sheer mass of firepower that even a mid-sized Imperial ship can deliver would quickly overwhelm a Federation ship.
Even when you consider that the Empire would only be able to devote a fraction of its fleet to the war effort - say, a sixth - that’s still more ships than the Federation can muster in any way, shape, or form.
Furthermore, as a war of conquest, the Empire can move from planet-to-planet with near impunity. The Federation can’t detect their movements through hyperspace, and they REALLY can’t send ships to intercept. Additionally, the Federation stands absolutely NO chance to invade Imperial coreworlds… with a given speed of about 1 year to cross 1,000 lightyears, they simply can NOT launch a conquest of an Empire spanning over 100,000 lightyears.
Transporters: As has been pointed out, these things can be disrupted by almost anything.
The Genesis Device: According to ST2, all data on the Genesis Device was lost when the Regula station was destroyed. As such, the Federation doesn’t have access to it as a weapon. Sorry.
Cloaking devices: A very excellent advantage, and I have no doubts that the Federation would quickly lobby to nullify their no-cloaking-device treaty. However, as it is, the only cloaking device they have installed on a ship is the Defiant’s, and that one is on loan from the Romulans. Given that the Empire can have Star Destroyers pounding on Earth in, oh, a week, that’s not a whole helluva lot of time for them to develop a line of cloaked vessels.
Face it, the only way the Federation stands a chance is by calling in their “superpowers”… Q, the 29th-century timeships, the Douwd (or however you spell it).