@Schwartz: none of that addresses the real issues with MSG ships.
1. MSG ships are also typically crippled on Capacity and Dissipation. Even if MSG was un-nerfed tomorrow (I have no idea why it was nerfed at all, it was hardly an abusable mechanic), it would still suck, because the ships that need it aren't equipped for "normal" shield stats and perform terribly.
2. While the Beam Armor idea has merit, it'd have to be 90% or so for shieldless ships to be even roughly worth taking, and shieldless ships would need better Armor / Hull stats and room in their OPs for defense against Ion weapons, as above.
3. This isn't merely a problem of, "they're sub-optimal midgame". It's "they're never worth deploying at all". Seriously, Hounds have been reduced to ships that I use for efficient cargo-hauling (and they're undercut there too, now). The Cerebus has literally no point at all past the early game, and you don't typically have HVD's / Heavy Maulers then (or are mounting them on an Enforcer).
4. There is no such thing as a "rare HullMod". Either it's effective enough to bother grinding for* or it's not worth the bother.**
In fact, I don't want to hear about "rarity" in terms of "balance" for SS ever again.
The only way we can have true "rarity" is by having some Uniques in the mix or by having a Diablo-style RNG data per-weapon / per-ship system that creates some true "rarity" in the statistical sense, etc.*** If the game would be better with some unique ships / weapons / Hull Mods then fine, let's talk about that, but let's not talk about "rarity" like it's an actual fix to the problem of an entire thematic class of ships.****
The whole shieldless-ships-as-theme thing should just work; it should be interesting and worthwhile.
So, what could fix these ships as a theme?
1. They could have built-in Hullmods that made them unable to mount shields ("Low Flux Performance", "Adamantium Armor Plating", "Hot Rodded" all sound like catchy names-as-explainations), but gave them serious bennies.
What would be worth not having a shield?
A. Being able to kite, because of range; perhaps they can have an improved ITU that puts them a size-class up, because "they do not suffer Sensor interference from shields" or some other hand-waving.
B. Being able to tank Armor for reals; 99% absorption rates at 100% Armor rather than 85%, 50% min rather than 15%; basically, make them really quite tanky.
C. Mobility; the Hound used to be uncatchable, pretty much; this isn't a bad thing, it gave them a role as "that ship you have to corner or make the AI screw up to shoot" rather than helpless vs., well, basically anything sensible. Hound with ITU / HVD was actually not horrible; it's horrible now because it's just going to get eaten vs. Beams.
D. Really good anti-Beam defense. Like, good-enough that they're a hard-counter to Beam-heavy fleets. This is a theme that should exist anyhow.
There are other ideas that might work, but the point is, if a ship's giving up Shields, it had better get a pretty amazing tradeoff... shields taking Soft Flux from Beams and not being vulnerable to EMP and getting buffed by Captain skills, etc., matter too much.
2. They could be universally given enough OPs to buy all the things to make themselves somewhat viable with MSG's terrible flaws... or go for all the Armor and Hull protection mods and other toys. And guns. This wouldn't break anything or require a new system of mechanics; they'd just be jack-of-all-trades ships, able to go for a variety of configurations. That isn't terrible as an idea; simply double their OPs, more or less, so that they can pile on Hull Mods.
*...in the sense of looking to see which Faction carries it and finding it after countless shopping expeditions- ooh, what fun!
**Having to waste your life on this Earth searching for something you need to make a core mechanic viable, given that this is RNG, is game design at its worst, imo.
***This is now not impossible, and I've even considered modding to Make It So, but I rejected it because it'll just encourage more boring grinding.
****Which it might be, in terms of power progression...