Interesting thought! Seems like it'd be hard to keep track, though. And you might have to do odd deployments like "this one cruiser, THEN a bunch of other stuff" to make sure you got exactly what you wanted. Manual reassignment is a bit of a pain, yes, but this seems like it'd also be a pain but in another way.
Stepping back, though - conceptually, I think it's better for officers to generally be assigned to a specific ship, instead of having a fleet of a bunch of different ships for every occasion with officers transferring between them. It's less hassle all around, right - neither transferring officers nor having to figure out what gets auto-assigned how when you deploy. And having officers be associated with a specific ship just feels more right to me.
I'm pretty confident that frigates will be useful in the next release, regardless - it'd be surprising if your 8-10 best ships didn't include one or two of them. Not only do several fleetwide skills have less of an effect when they affect too many deployment points worth of ships, but - why would you have, say, 10 Paragons or some such? It's technically the most power, but you can't deploy that all at the same time anyway, and they don't help for determining deployment points any more than having those officers in other ships would. In fact, if you have those frigates cap something, you'd come out ahead deployment points wise.
And when you consider that frigates/destroyers will provide bonuses to your *other* deployed ships (via some officer skills - Gunnery Implants provides an EW bonus when in a frigate/destroyer - larger bonus in a frigate, and via Coordinated Maneuvers)... And, also, it's possible to boost peak time - both specifically for frigates, in by flat amounts that matter more for frigates. And the EW skill gives a flat bonus instead of it varying by ship size. I think there are *a lot* of different factors working together here - some of them making frigates better, but more importantly, other factors making them into more of a force multiplier.