For the Pegasus taking 3:1 odds and having to run, IIRC the Pegasus was lured to a specific point, then ambushed. Given the point to point FTL capability both sides have, First Strikes like that would be the norm in a war, meaning both sides would try to keep their military installations secret, and likely moving. (though why no one developed jump nukes is another question)
Exodus pt 2 observations:
Galactica was expected to be able to take on two Baseships, which is interesting. Galactica is an older Battlestar, against two new Baseships. Pegasus (with a skeleton crew) is able to engage 4 Baseships, though they do lose after abandoning ship. If Lee had been smart enough to have the FTL core prepped, they could have jumped out after Galactica and the other civilian ships had left, leaving one dead Baseship, three damaged Baseships, some severely embarassed Cylons on-planet, and two heavily armed Battlestars, instead of one. Strip whatever you can from Pegasus and transfer it over (include a comment about the spine taking a nasty hit), so Pegasus does get lost (so they can use the sound stage for the Cylon ship).
For the combat capabilities of the Battlestar series, I'd see them as using fighters as defensive and precision strike vessels, rather than direct combat. The heavy gun batteries are what Galactica uses when it wants to kill an enemy ship. For the pods extending/retracting, that could be FTL limitation, though the ability to shelter the flight pods behind the heavy nose would be nice to help prevent them taking fire (Exodus pt 2 had the Cylon missiles diverting around the nose before they hit the Galactica).
Overall, I'd see Galactica as more of a Battleship with defensive fighter (and Raptors for long range search) component, rather than a carrier with offensive weaponry.