This always depends on how far into the game we are, what kind of fleet your opponent has, and what faction you are, but there are some general guidelines I can give.

First, focus heavily on damage dealing units, such as LRF, heavy cruisers, or bombers.  Rounding these units out with light frigates, flaks, and fighters is a good idea.  Back them up with support cruisers, particularly subveters, guardians, and hoshikos.  Choose capital ships to provide maximum fleet support.

A typical mid-game fleet might be 60 or so LRM, 20 hoshikos, 10 flaks, and a Sova, Akkan, and Marza for your capital ships.

Are 10 flaks really likely to be enough to protect against the SC you typically seem to encounter in a mid-game fleet?  At one time, and I have no idea what version it was, it didn't seem to me that the flaks were doing much and I began countering SC with SC.  From what you just described it seems that flaks must be pretty effective -- maybe I will have to give them another try.

No, it's not enough.  These flaks are designed to suppress mild amounts of strike craft and provide a small amount of support against larger strike craft groups.  It is not by any means an appropriate number against large groups of strike craft.  This fleet is very much focused around their LRF, meaning its about closing the distance and winning a shoot-out with the enemy.  Against a kiting carrier group, I'd definitely phase in some cobalts or a much larger proportion of flaks.  Keep in mind this fleet also has a Sova which provides some fighter presence.