Hmm well a smattering of AC's/LRMs and MGs on older vessels like say the Monsoons, whilst later ships get LB-10's, LRM with Arti IV and AMS, or replace LRMs with clusters of large lasers and the like. Smaller ships might go for batteries of large and medium lasers vs autocannons and LRMs to save space (not that with that much cargo space they actually need space to be saved)
Or for older ships go and do what the Dreadnought class did, quad mounts of AC-5s and AC-2's and MG's for point defence. The Dreadnought had a pair of quad AC-5's and a pair of quad AC-2's in each section so for its time against 'armed shuttles' thats not at all bad. Sure its NOT damaging at all but its flavourful if you like to picture this;
Also re the Aegis, she was not under-armoured, she had more armour than pretty much everything until the Black Lion moon walked onto the scene.
If I was to change the Monsoon I'd add a trio of Quad AC-5's to each section and 6 MGs per section. As they count as half against missiles it would be the equivalent of 3 AMS. I'd also put a quad or even quin NAC-10 in the FL/FR AL/AR and stern arcs to give her some more long ranged firepower. You've got a huge amount of tonnage to work with so you can use it.
With tighter designs like the Black Lion I'd keep her pretty much as is, add a LF battery and mobile HPG, see if you can another Barracuda launcher where they are plus ammo, as well as either some triple large lasers (or ER large when available) or triple large pulse for anti-fighter defences. This won't affect her cargo too much and you've got 4 dropcollars so just have a mule with you.
With the McKenna, add marines, add a mobile HPG, and up her armour to at least Texas levels whilst adding some LB-10s and large pulse or ER large laser turrets and a good smattering of AMS across her, whilst doubling the ammo load (at least). I'd even think about doubling up on the AR-10's and at least doubling their ammo, and add a pair to the AL/AR arcs as these missiles really are your main anti-fighter defence.
The Lola III's firepower is fine, add a grav-deck for the crew, up the armour so its at least 50 on sections (she's a 'heavy destroyer' after all). Add a mix of medium and large lasers (two of each type per section) along with AMS for close in defense. Maybe add another NL-55 to the AL/AR but otherwise keep the rest. Grav deck would be nice though.
The Essex II seems to be a cheaper design but she's still a tad lacking. Up the armour so its at least 40 on all sections to start with. Maybe double her fighter capacity to 12 and keep the 4 shuttles. With the NL's and Med PPCs, i'd make the NL-35's at least quad mounts and add another Med naval PPC to make them triple mounts. Some LRM's for anti-fighter work and some AMS. Oh and at least double the fuel tanks.
The Whirlwind is a bit tighter. Whilst i'd not bring her armour up to Clan levels i'd at least want the sides and rear to be 40. Add a pair of NL-35's to the FL/FR and swap the positions of the NAC's and gauss. Put all three Gauss in the nose and the NAC-25's in the FL/FR .
Congress - Make the NAC-10 mounts be quad mounts at the cost of the NAC-30s, double the ammo for the missiles, add a pair of Killer whales for 3 in the bow. In the FL/FR AL/AR i'd add a quad NL-35 mount whilst also looking at doubling the fighter capacity to 12. She's a patrol craft and her fighters will be her eyes. Marines for boarding actions, a mobile HPG and double up on her large lasers and add AMS. I'd also look at making her a 4/6, she's a bit slow.
Really the only ship you can't significantly change without a complete re-working is the Kimagure. They have no cargo to work with. Only thing i'd do is replace the small pulse lasers with 3 AMS per section and some ammo.