What I was thinking was:
-Korolov shipping missions are a 'hook'. They're linked to by the tutorial quest now, and they're a good source of early-game cash. However...
-They escalate quickly into encounters with frigates, which often attracts the Kronosaurus early
-Once you kill the Kronosaurus, you have no more missions
-Then you hit charon, with no warning, no setup, and it's virtually impossible.
-Also, the rewards suck. You can achieve the impossible and get an omni-particle cannon...which is generally a worse gun than you'd have by then anyway, by DPS. It should give the player guns they wished they had 5 minutes ago.

So the problem really is balancing that final battle, putting it into context, and making a proper questline, like so:
-First, the player does regular korolov missions. These should be a bit easier to get: Maybe even return to having a K base in Eridani to get things started?
-Once we've proven ourselves (Journeyman rank + X Fortress kills), we start getting the option of missions that give some background on the fact that the pirates are starting to push against the shipping companies. Maybe even raids against the stations themselves, where the player has to intercept and destroy 1-2 Drakes with Viking escorts.
-The Kronosaurus will have multiple reasons to appear: If we kill enough frigates, fortresses or drake assault parties (during missions), the ship will be sent to kill the player. If we're doing special missions, we will eventually receive a mission to lead a wing of Ronins to kill it, just in case it hasn't turned up already (obviously, we do not get this mission if we've already killed the Kronosaurus).
-"Legend" rank can be attained by beating the escort record, killing the Kronosaurus, or completing X "save our station!" missions.
-Killing the Kronosaurus nets you a bit more cash, as well as what you got for annoying it in the first place.
-Once you're at Legend, you don't get escort missions, but you can still get special missions.
-If the Kronosaurus dies, you can get a mission to escort an EI100M with a search team to the wreck. You automatically get this mission offered (with an option to "let me repair first") when you dock after killing the ship yourself, or completing the "kill the kronosaurus" mission. After fighting off pirates and other scavengers, the search team scours the wreck and uncovers the plans to the charon assault. We get some exposition, then a mission to take some wingmen and go and save it.
Modifiers to the Charon mission itself:
-The base itself should have some initial defenses. 4 turrets, and possibly some Quad titanium barricades. However, our actions earlier dictate whether these are still there.
-If we've destroyed charon fortresses, fewer attacks will have been mounted before we get there. The stations barricades are damaged, but still there, as well as 1 or more of the turrets still working. The station has 250HP (its maximum).
-If we have not done these missions, the station starts out effectively as it is now: the turrets are wrecked, the barricades are gone, and the station has been reduced to 150HP by a previous attack (yes, the station ingame right now has 100HP less than a regular K base).
-For each "intercept raid party" or "kill fortress" mission, the attacking force could be reduced in some way. Not sure how that'd work though.
-If we have not killed the Kronosaurus, it is commanding the attack. It turns up after the gunships, but before the Drakes. If it survives the attack, it raids the korolov base briefly then leave, it then docks at the main fortress with an escort of Corsair-IIs.
-Regardless of whether we save the korolov station or not, we should get a charon base map from them.
-If we've got a wing from the other korolov stations, they should be reasonably tough...possibly NPC wolfens....and accompany us until we've dealt with the fortress. They leave automatically (and give a bad mission ending) if we go past St. Katherines without killing the fortress first (INTO St.K's is fine. Just no further.).
-The korolov base itself should have fewer guards, but have them be of higher quality. Corsair-IIs in the gunship waves should focus on the guards, and not attack the station until the guards are destroyed.
-The charon sub-fortresses should be significantly harder to attack and kill.
-The fortress itself should also be a bit tougher.
-Finally, mission rewards should be good. A hefty credit reward (25,000-50,000) for dealing with the fortress, equipment (the Type V deflector, X-Ray Laser, or other similarly awesome gear) for saving the korolov station (no consolation equipment prize if you don't). And automatic promotion to "Legend" for doing either.
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A bit of a messy post, but I'm running late this morning anyway. I'd like to hear other people's thoughts on Charon, since I know that it's been annoying for a lot of people for a long time.