Tell me what you want, what you really really want! ...Oh wait, you just did.
You want a small ship with a high mass lock factor?
Yep, because mass lock is based on... mass, not size. A super dense, small ship could theoretically have a high mass lock factor.
Back in the old MS-DOS days, there was a very difficult game called Epic. Basically in the far future, the aggressive Raxxon race is trying to exterminate humans, and the sun is about to go supernova. Humanity's only survival option is a mass migration through hostile Raxxon space to the nearest habitable world.
To accomplish this, humanity uses their entire stock of... well, a super-rare meta-alloy, basically, to engineer three heavy superiority fighters, which you, as humanity's best pilot, must pilot and safely see the convoy through to their destination in a variety of harrowing deep space and planetary combat missions. Great game, never did beat the final battle where you have to save the human fleet from literally hundreds of enemy spacecraft.
But the Epic fighter was essentially what you are asking for OP, a capital class vessel contained in a fighter-size hull, and I like the idea. I still fly small ships also because I love the way they handle, but their actual utility rapidly disappears as one progresses through the game.
I think the problem could be hugely and easily amended by changing the number of utility slots on ALL ships. There are some ships that you fly and think, "Based on the cost and performance of this thing, and the surplus of power, it really should have 6 utility slots, not 4, etc."
Really power concerns are the only limitation for having more utility slots. I actually think most ships should have more utility slots than is actually practical, and the end user can choose to have more utility slots, or more power-hungry modules, but not both. I envision a future where the average ship flies around with several empty utility slots, and where specialized ships can equip more utility modules, but at the expense of some other functions.