You're right that it makes a heck of a story element. That mission from Lady Centrella to get to Axylus via the pirate point was, hands down, the best mission in the campaign for me; well worth the price of admission, It was like I was risking it all on a secret nobody else knew about, on my own, with nobody else who was going to save me if it all went FUBAR. Maybe I'm unrealistic to want that kind of feeling every day, and thinking the pirate points as a regular feature would give me that, because then it wouldn't be anything special.
But, for me at least, the main appeal of pirate points is that the ships who use them travel them in secret, and I kind of like the thought that I'm in on some little secret hardly anyone in the Reach knows about. It makes me feel like I have more to offer the clients than simple battlemech tonnage, but experience that shows a deep knowledge of the reach that my clients lack. I imagine there's two starmaps of the Reach: the one Sumire and every other captain knows about, and the secret starmap, that only that pirate agent dude who says "You want to get paid, don't you?", other members of the criminal underworld, some house intelligence agencies, some high-ranking ComStar agents, and several old and cagy mercenary captains like Jamie Wolf, Morgan Kell, and Wayne Waco know anything about, and even these agencies and people don't know the extent of all of it, but bits and pieces here and there.
The main reason everybody isn't using the secret starmap is because it's secret. It's the starmap you use when you want to transport things you shouldn't be transporting. Drugs. Weapons. LosTech. Commandos. Wanted criminals. And political figures like Lady Arano when she fled after the coup. Nobody, outside of a few people, know exactly when the ships arrive and leave, and exactly where it came from or is headed to. And space is a big place. There's a whole lot of real estate there in a solar system you could plot a jump solution to. And unless you are in on the secret, you'd never know where to look, or when to look.
You'd think the navigators would become really good at plotting solutions if they were jumping to and from a system on the regular, because they would, over time, familiarize themselves with all the quirks and variables, kind of like a smuggler on a small plane learns how to land the plane on an improvised landing strip in the pitch dark, or a guy in a boat learns how to read the currents and the tides, and when the coast guard patrols arrive. It ain't safe if you are doing it for the first time. It ain't 100% safe at any time. But it's been going on for so long, it's reliable enough that whatever criminal organizations use it as a trafficking route can plan accordingly, make sure the shipments get to where they need to be, link up to the KFFC booms as a science, and go. The ship might even have an LF battery or other LosTech that gets it up and out fast. And it's this routine, carried on in secret, that eludes the authorities. Maybe ComStar knows, but it ain't talking. It might even be in on the whole thing.
That's really meta, and not mechanical so much, but it would be interesting if, over time, you could learn about these secret routes, and use these secret routes, so you might not have to jump four systems to go from, say, Detroit to Weldry. You can learn about a pirate route that goes from Detroit to Herodotus that can get you to Weldry in two. Truth is, it's been there all along. But you only knew about it when you did a favor for the "You want to get paid, right?" guy at a flashpoint, and now that you know about it, you can use it.
You do a flashpoint for Kurita, and part of the flashpoint involves boarding a captured Davion dropship, taking it through a pirate route into Liao space, and blowing up a fuel depot to provoke Liao into attacking Davion. Now you know about the pirate route, so you can use it. Your map is now a whole lot more detailed and complete than it was when you were a n00b driving that Vindi they gave you at the beginning of career mode.
So that is how I might incorporate the pirate points, as a kind of easter egg or McGuffin that makes you feel like you've joined a secret club, or that you've got what the equivalent of "street cred" in the Reach. It isn't like it's game breaking; by the time you get around to uncovering the "secret starmap," you've already played out any reason to be forced to jump four systems to reach Weldry from Detroit. You have, by that point, earned the right to do it in two.