In terms of Console layout and special abilities, the Science one I like the most for a few reasons (Sensor Analysis and 2nd Science Console).
The Command has Sensor Analysis. That thing keeps stacking up the longer you target an object, as it stacks up to 10 times, you have better DPS, but it relies on the fact that that object is alive for that long. Plus, the Subspace Snare it awesome for dragging objects in front of you, but unless you have something like the AutoCannons from the Tactical, then its not very useful.
The War has the HoH'SuS. A handy little thing if you ask me, especially with Subspace jump and Quad Cannons, but its squishy. Add to that, the extra Engineering console won't exactly grant you DPS, but the War is interesting for the BoP at least.
The Tactical has a 5 Tactical Console... the only KDF ship that has it. Add to that, the mega AutoCannon at the front that does enormous DPS. The thing about that is, you have to turn your ship around, which is extremely difficult.
Based on your reasoning, your preference and the process of elimination for all of these varients, I'd agree with the War Cruiser. The reason for that is because Sensor Analysis requires target for long enough, Subspace Snare is a support ability that needs a follow-up, and the AutoCannon is difficult to point.
T5 Ship Comparison Spreadsheet
Play my missions on Holodeck!
Return of Ja'Dok Series (6 Part Series)
Enemy of the Exile Series (4 Part Series)
Task Force Ja'Dok Series (3 Part Series)
Personally I think the Command variant, the other consoles might be better but ship wise I think the Command is the way to go.
Defense wise all three are around the same...the Command has +10 to shields so still get a little umph to defense. For offense it does give up a 5th tac console but the sensor analysis helps make up for that a bit and allows you put another console of your chose in there instead of just another weapon console.