There is a much better Romulan weapon than the Mini Plasma Disruptor - the regular Romulan Plasma Disruptor - it's similar to Federation phasers and has 10 levels.
The top Romulan weapon is the Plasma Torpedo - but it's only good if you can get away the first shot and are in close range - and ofc, if you can hit the enemy ships.
The Klingons I think were vastly underpowered in 1.3.5, or at least it seemed that way.
Ofc, the Federation is still tops overall of the regular races. However, I haven't tried the most recent Version of the mod yet so I cannot say with any certainty that this remains entirely true in 1.5.1! Actually, I think the Defiant ships need to be made much, much, more expensive (they were way too awesome in 1.3.5 for so little resources) and the Juggernought size ship needs to be dropped. There are some other ship-size issues but I don't have the exact figures handy so I'll wait to later to post about them.
One thing I will suggest is the reduction of the mounts in equal size/damage ratios. i.e. twice the size gives twice the damage. If a true leaky shield system is used, the advantage lies in the initial punch for larger ships as you'd expect. Smaller ships need to be made more practical in the mod, so their defense bonuses and a minor accuracy penalty to the larger mounts would go along ways to balancing it out.
Also, there seems to be a half attempt at leaky armor (some components have low, low, structure points as you expect, while others do not) - but at the same time all the armor has the damaged first ability so it is kind of a mix-up.