It was a humanitarian mission, not combat. I doubt any of those ships were sent for support or defense of other ships, but to help Vulcan.
Okay; I will give this to you that Trek doesn't work like that (I could counter with Dominion War examples, examples in the movies like BoP commander calling the E a "battleship" etc. and the obvious different roles of smaller ships compared to larger ones) but I will give it to you that the Federation likes to build really big general-purpose starships. Still, Spock's "we are not prepared" means he knows and realises what it will take to defeat that kind of attack. What that means we don't get a chance to see. The Romulans in Enterprise had small fast manoeuvrable ships that could dodge phasers and photorps, so presumably there's a way to counter them with enough "prep".
Because the Swarm were new enemies. New enemies don't have 50 years of definable traits like the portrayal of Starfleet does.
New is fine, but there's certain characteristics which need to make sense in Sci-Fi movies... presumably the Federation doesn't have pylons holding nacelles because they like having a huge structural weakness, but because that's what it takes to make a warp field. Things like that. It would be jarring if all of a sudden fighters became the main point of ST. Not that I actually have a problem with new aliens or new technology, but it is certainly a gap. The only way to reconcile it is to say, had shields been effective, the fighters would just have bounced off or blown up.