I actually have a slightly streamlined version for the project I have been working on:

Tactical Micro-Jumps: A vessel equipped with Hyperdrive Special Equipment  may choose to move across the game board using a “Tactical Micro-Jump” rather than issuing standard movement orders. The procedure for doing so is as follows: The Hyperdrive is activated in the Orders Phase and a target hex is chosen anywhere on the game board. Since the distance being jumped is very short, it is not necessary to "charge" the Hyperdrive as in the normal rules for its use.

On the Movement phase, roll a D6, and if it comes up 1, the Hyperdrive stalls and the ship doesn't jump and follows the same course and maintains its current speed (no "backup" movement orders are allowed). If any other number is rolled, the ship immediately jumps to hyperspace. If the roll was a 6 the ship returns to normal space exactly where it intended, on a 4 or 5 it misses its mark by 1 hex, and on a 2 or 3 it misses its intended hex by D6 hexes. If the target hex is missed roll a D6 for bearing of the miss, and go clockwise around the target hex with one being on the "top" of the hex.

Ships return to normal space on the same bearing and with the same velocity that they had when they made the jump. Following a tactical micro jump or even a Hyperdrive stall, the ship cannot initiate Hyperdrive startup (of any kind) on the next turn.

I think you could use something similar to this for "jumping in", even if you don't want to permit tactical jumps. I think if you use it for jump-in you would have to also make some notation for facing and initial velocity, unless everybody arrives at relative rest. My thought would be that if all of the ships in a particular setting had the ability to do something like this, there would be no reason to change points/costing at all.
Cheers,
Erik

shouldn't it be so?

Since it is Starmada and everything is truncated or at least scaled for simplicity and playability maybe the best option is allowing ships within a  certain distance (1 or 2 hexes?) to enter the jump point when it is created. The vortex would be placed anywhere up to 6 hexes from the creating ship. Hmm, depending on the scale you intend to use, you could use a size 1 minefield template to represent the vortex and any ships in or adjacent to the point can jump, something like that. Until the shadows come along and disrupt your jump point that is 
Cheers,
Erik

My idea is to use something similar to ACTA combined with the charge rules from Starmada.  First thoughts are:

Once charged you place a jump point within 4 hexes of arc AB of your ship (not sure if they have to be opened forward in B5). 
Then ships can move through it via the 3 sides it's facing. 
At the end of the movement phase where the opening ship goes through, it closes.

I think I might reduce the time it takes to open, and there some other details to flesh out but this is the general idea.  The problem is balance and points values.  Not every ship has a jump engine, which is why it needs to be balanced.

Ok, so I think I've sorted "jumping out".  I've mulled over what I posted and I'm going with that until playtesting shows otherwise.

However, back on to my original post, "jumpin in".  I've been thinking about this more, and one option is to simply handle it via the scenarios rather than on particular ships.  Most encounters won't allow jumping in, as you'll be meeting in space with your fleet and nothing will be available to come in afterwards.  Therefore I don't want to increase point costs for something that is not used.  For scenarios where it is allowed, such as amushing, planetary assault etc.. then the points allocated to the attackers can be modified to acount for jumping in. 

ACTA did something similar.  Most scenarios did not allow keeping forces off the board.  I think this also fits B5 as I don't think you can detect enemies from hyperspace, you just jump to a certain point. 

Anyone see any flaws with this?

Yes, so I'm going to handle this on a scenario by scenario basis, rather than having to put it as a point cost to all ships. The forces with reinforcements available will be adjusted for the benefit of having suprise attacks available. 

An simple example would be a planetary assault scenario:

Defender 1000 points on board
Attacker 400 points on board, 400 points in hyperspace. 

I've no idea about points yet, but you get the general idea.