I'm looking for a little advice on how to handle some enemies 2 characters have from character creation. They are a brother and sister pair on the run from a corporation (wanted quality) and also have a 5 point enemy each. The story being that they were framed for something by the enemy and this earned them the wanted quality from the corp. So the corp is hunting them while they look for the enemy to clear their names. The initial plan was that it is the same enemy for each but this feels a little weak to me. I thought that I could use the enemy in this case as 2 separate enemies, say a team that framed the brother/sister and make each enemy as a separate character, or combine the enemy into one more powerful character.
I'm using the enemy rules from RC with a 4 in connection and 1 in incidence. This makes a fairly well connected enemy that really doesn't care he is being hunted by the characters and still has enough juice to make their lives difficult on occasion. So what do the GMs out there think, 2 enemies that work as team against the brother/sister or 1 more powerful enemy? Or some other idea?

I say 1 more powerful enemy. Furthermore, enemies aren't being hunted; they are out to get you. I'd revise your stance a bit to go along these lines:

Enemy knows that the kids can blow the whistle on something he did. Hence he framed them. However, now they they have gotten away he needs to make sure that they are dealt with before then can find whatever they need to bust him.

And 10 points in an enemy is quite a regular, powerful, threat for the entire group. Especially if this enemy has the backing of a corp.

Well, you have the opportunity to create one heck of a powerful enemy, which will have substential ressources to damn your players The choice is kinda theirs since they're paying the quality: either they tag along for one major powerful enemy (two enemies stats built into one), or they each have their own enemy (why not another pair of siblings ?!?!). In all cases, your players will tag along in trying to get rid of the enemy.

In both cases, I strongly advise you create a solid background for the enemy(ies). Make sure you can build devious plans like:
- Run interruptions
- Killing the Johnson just before the players come back for their remaining cash
- Have the enemy engage the players through a Johnson and send them into a suicide mission (without telling them, of course) or do a devious plan that will help the enemy (suddenly, those hard earned Karma points don't taste the same )
- Use false rumors
- Get the contacts involved
- Have the enemy send a tip to Lone Star
- Make it personal

However, give opportunities for your players to hurt the ennemy (I say hurt, not kill).
- Financially
- Getting rid of his contacts
- Stealing a contract from the enemy
- If the players want, allow them to take the "GM lead" and devise a plan to hurt the enemy (that's motivation)

Remember, revenge can be sweet

It sounds alot more like they have the 'vendetta' quality than the 'enemy' quality. Vendetta is character hunts something, enemy is something hunts character. I suppose 'enemy' still works, but if they stop going after him, he should decide to go after them. Just so long as the quality continues to apply as long as he isn't delt with.

Personally I'd also do a single more powerful enemy than two weak enemies. Basically just make the same kind of enemy you would for a 10 point enemy quality and then have him work against both characters.

Yes and no. Vendetta requires you to get the Enemy quality as well, and have the Enemy with an Incidence of 4 or higher, meaning they'll show up a lot (this is a bit of confusion for some, Incidence doesn't mean powerful, just means you'll run into them a lot). And the enemy will follow the same rules of creation as the players (i.e. 400 BP for standard creation, higher if a higher BP game, lower if a lower BP game, etc) and the other points the character gets back from the Enemy quality cover the kind of connections the Enemy has. So if they want to share an enemy, go for it, that enemy will be on the same level of power as the characters themselves at all times, and has the power of Hand of God to show up when by all rights they should be dead.

I like your ideas PatB. I was going along with the idea that the enemy is going to screw with them but I didn't want it to be the focus of most runs which is what you get with a high incidence. This enemy won't have corp backing however. The wanted quality is related to the frame job but the framer (enemy) is using the characters as patsies and has no relation to the corp beyond having stolen something from them and framed the characters for it.
Anyway, some nice ideas here. Keep them coming. I'm not totally convinced on one powerful enemy. (pro, easier to make one than two and is always fun to GM, con will mess up the rest of the group and prove hard to deal with), while 2 enemies require more work but not quite so many resources on the players' part to deal with. It is just a 5 point quality each after all.
I find that by using the advanced contacts rules anything beyond a 5 point enemy works better as a group or else shows up all the time. I had also thought maybe a group. Both of the characters are magically active if that adds anything.

Perhaps look at the group contact rules and apply that to enemies. You don't have to do a 5/5 enemy that way. You could do a group enemy which would make it fairly powerful, yet also keep the incedence down.

Just be sure to make it clear which character(s) the enemy is going after. Unless the entire team took the same enemy, he should only be screwing with the lives of those characters who got build points rather than the entire group. Unless the enemy is to be the focus of a game session/run, it isn't really fair to punish the other players with constant harasment by somebody else's flaw. Screw with those PCs, contacts, gear, life style etc, rather than everybody.