I was hoping for better constructive thoughts to help design better gameplay for both factions. Instead I get absolute thoughtless garbage.
You do realize that in order to be effective this would take at least 2 ships alternating their scans. In a 5v5 that is 2 science BOs in a 5-ship fleet. Two less buffs/heals/debuffs.. At the first tier that is a huge loss to even an organized team. You just gave up a tractor beam, a jam sensors or something else which puts you at an advantage against your opponent. There is no way to close on an enemy ship which want to evade while doing this scanning which would keep your energy levels high enough for effective combat. There is no good way to keep the fed ball intact and give chase at full impulse to ships which are faster than your cruisers. Feds would be led into countless ambushes instead of their only option being to sit and wait.. and you think this unfairly penalizes the Klingons.
OK 2 sci ships 3 cruisers. Its what works really well against klingons, and nearly impossible to kill if the teams setup for pvp.
Sci ships lose 1 ability each to do something needed in PvP? fine, BoP loses 1 officer slot, so your still 3 BO slots up across a 5 man.
Play the game for a month, re roll characters as often as possible using different skills/builds and ships each time. You'll find thats theres bugger all in this game that has'nt got atleast a couple of counters.