well we intend to follow the basic format and rules (other than the fact we may have stats/skills like 5.2 and 4.7), but I can honestly see a bunch of issues:
- we will be biased towards combat/communication skills, so certain skill groups won't be featured much in the game (such as knowledge)
I had a feeling about this. My guess is that language skills will not be necessary, neither will some physical skills to simplify gameplay... like gymnastics. Also, the majority of social skills will probably be omitted (with the exception of perhaps con and negotiation). Does that mean that crafting will be handled skill-lessly?
- we will probably rack up more contacts than your usual runner, but less stuff otherwise
I saw that coming. That means that a lot of the minor purchases that runners make... datachips, mapsofts, metahuman customization and the like will be implicit in the game.
- magic and hacking will work differently (as they need to be on equal footing in the action map), so not sure about the corresponding numbers etc.
How will you do this and match them at least somewhat to the playstyle of the characters in the tabletop game? The two tend to be dramatically separate in gameplay; hacking is a more subtle affair, while magic is very... artillery-esque?
I'd say that you just have to give hackers room to be as versatile as they are in the RPG. Allowing rigging and plenty of drones (at least as much as the usual subscription rates in the tabletop game) will go a long way to balancing them out. Giving hackers plenty of on-map cameras and nodes to hack will also help. Really, the best way to balance the two is to make sure the map is catered toward hackers being present (which shouldn't be hard, considering that a wireless mesh of devices is standard fare for the setting now; it would almost be out of place for the game to have matrix dead zones)
- we may start from a lower base of initial points to make up for the low power level progression in SR
This is fine. What might be helpful to players that want conversion between games is if you use some sort of character title to label characters that are about equivalent to standard characters in the tabletop game. So for instance, when my technomancer (you must have technomancers in your game) gets a certain level of attributes, skills, complex forms, nuyen, contacts and equipment, I could get the "Veteran" character title, which informs me that my character is ready for the tabletop game.
So I would say you can probably build a similar P&P character from an SRO character, but especially once progression kicks in, it won't be copy paste.
And honestly, your P&P character will have much more color I would assume 
As long as conversion takes minimal effort, it's fine.
Such things as "take your MMO attributes and skills, round down to a whole number" are fine conversion requirements.
As long as it doesn't require it's own book to make the transfer, it shouldn't be an issue that we'd all fret about.
But character conversion is practically a prerequisite if you really want to cater to the tabletop RPG fanbase. Not doing so would be like trying to have a charity bluegrass concert for fans of metal.