The problem with that is that you're talking about 1v1 PvP, and what people do the most is 5v100 PvE with a time limit. Those are radically different environments, and sci abilities really don't do much in the latter one. The best you get is GW, which can give 20 seconds of hold and 1k DPS, and then goes down for 40. The power drains are feeble, and FBP and the sensor abilities don't even work at all on the many targets that don't shoot back. The Vesta's Aux DHCs are the only boost PvE sci has gotten in the past year (the tac heavy fleet ships aren't really boosting sci), and my suggestion is simply a way for them to better synergize with sci abilities.
While I admit, it would be rather nice to have everything available as an aux weapon (maybe as a very rare drop with the ability to run on aux instead of weapons power taking a mod that could have otherwise been [Acc] or [CritH] etc.), I can see a need for limitations.
That said, It would be nice to at least have aux phaser turrets.