Well, you're onto something there. To be honest, I didn't play with shuttles much recently, but I have to agree that lack of any standard ability and relying on just one singularity power doesn't really measure up to other factions' small craft.
I didn't really pay attention to this in the game, but if Romulan small craft do in fact have only 40 base subsystem power, like the warbirds, then this is the first thing that should be fixed. Warbirds are far more powerful ships, with 5 singularity powers at Tier 5 so it's somewhat justified for them to have -10 subsystem power. But small craft? Those things can barely do anything already, with little options to increase their power levels. Not only that but they only get one singularity power, not five. And even then this singularity power requires absurdly long charge AND recharge time - far longer than what other factions' small craft have at their disposal.
I've purchased the Scorpion Fighter some time ago and tested it during the Atmosphere Assault mission and I was really surprised how weak it was. Even with two energy weapons the Singularity Overcharge didn't seem to do much, even at 5th level. And with just one boff station there wasn't much I could do, even though this was supposed to be a fighter. In the end I thought of changing to Kestrel, but now I'll wait for the Commander's Gig to come out, just for lulz.
Overall, yeah, there seems to be quite an imbalance when it comes to ROM small craft. Either they should have standard 50 base subsystem power level, OR they should receive yet another integrated active ability, just like all the other shuttles do (so Tractor Beam for Kestrel, Rapid Fire for the Scorpion, EPtS for the Jarok/Talon) OR have a second boff station. As it is now they are penalized severely with 40 base power, one weak singularity power with long cooldown and no other active ability or 2nd boff slot. The only thing they do get is the cloak, but honestly that isn't much, especially when compared to something like To'Duj fighter.