Federation "Subsystem Targeting" for Defiant & Sovereign- Descriptions are identical for levels 1-2-3. Duration does not increase nor does the damage. What changes do the levels affect?
It's an on hit weapon modifier. The chance of disables and extra damage increase with levels, 3 being twice as often as 1.
Klingon Opening Capital: All abilities selectable from Level 1. Is this deliberate?
Ion Torpedo is not available from level 1. Did you get the wrong ship perhaps?
The Klingons and Romulans both have a fleet decloak ability, which is indeed initially available while being a single level ability. In the Romulan's case, the third level of Enveloping Shot requires level 6, as an ultimate would. The Klingon version has no such case, simply lacking an ultimate capability.
Dominion Leviathan- Has an ability which just gives 1% cool-down which doesn't increase with levels. Really? 1%? Really?
The asshole in me is strong, so I'm leaving this one obscure. Disloyalty. It does increase though, larger radius and the cooldown increases to 2%. That's not the main function of the ability, however. Those who wish to explore and solve the mystery are free to do so, but I'm loath to spoil my fun.