*ponders what would happen if he tried to base the entire LR fleet out of Buffalo*
*fails*
You're on the right track to a good idea, but there's a couple quirks- first, about half of the criminal groups in Sirius fly bombers that are the size of gunboats, and if size is the issue here then they can't land anywhere. Also, until IDs are moved around to be sold at more bases, should your RP need you to change ID you wouldn't be able to with a larger ship.
As for caps docking on planets, they can go for basic repairs and restocking via the mooring fixture (the docking animation is completely off, don't pay attention to it) but for any serious work, look at Battleship Yukon- it sits in planetary orbit getting crews sent to it, as opposed to hanging around the mooring fixture.
Speaking of mooring fixtures and docking rings, Praetyre, Gronath and I had a rather lengthy conversation one day and came up with this-
<massive rant on the way Sirius works>
Ships in Freelancer (with a few exceptions) are unable to fly the way planes do in our world- they are space superiority fighters after all, and not designed to be aerodynamic in the slightest, not to get started on transports and capital ships (which are basically bricks with guns). From the developer Liberty Backstory we can reasonably assume that docking rings are a type of space elevator, carrying smaller ships from the surface to space and back down. This is further reinforced in a slightly ooRP way that large ships can't dock with the docking ring- they must attach to the mooring fixture and go down via shuttles or possibly a passenger section of the space elevator. The only ships capable of going down and up freely are specially designed shuttles, probably only a little larger than starfliers and similar to today's "space planes" in function. This is how criminals get aboard planets, as well as how the junkers do their serious smuggling (docking rings ostensibly have customs).
Now, Andre DelArco brought up a good point when he asked about this- since the fighters and freighters and whatnot aren't aerodynamic, but we see them flying around in atmo in various cutscenes, how does that work? Here's how. Go to the ship dealer, and look under a fighter. Notice something? The little white ring thingies? They're also there when your ships take off to head for the space elevator, and they make limited appearances in cutscenes where they are used to levitate the artifact. How it works is irrelevant, but the small ships capable of flying around at low altitude use a sort of "ground effect" (the helicopter bit especially) that allows them to use this hover technology to keep them afloat, so long as they stay fairly close to the ground. Fighters and freighters, being designed to mostly rely on the docking rings, are optimized in other directions than fully utilizing this, and so cannot use this to escape atmosphere except on the smallest of planets.
</massive expose on how Sirius works>
Hope that helps. Feel free to ask questions about it, my skype is sovfalcon.
Now, back to the original issue- yeah, it seems a bit odd that big ships can dock onto little bases like West Point. The "RP answer to a somewhat ooRP activity" is that these stations have mooring fixtures too- notice that big ships always head toward the top sections of these bases. Ostensibly they moor alongside the base and unload, rather than going inside (!) the base.