Only Auxiliary Control should require a level 2 officer. This way, you can still make smaller ships like corvettes and frigates that you'll likely have many of be commanded by officers rank 2 and lower, which sounds about right. I don't think frigates these days (at least true frigates, not oversized psudo-destroyers) are commanded by full Captains.
I also think tonnage and/or crew size should play a bigger role in deciding what level of commander you need in Commerical ships. A 500,000 ton super-freighter with over 2,000 crew should require a full-blown Captain.