I haven't built a 4th ed character, but I generally follow the same pattern regardless of the system.
Figure out the type of character you want to play (I.e. do you want to play a decker, heavily cybered tank, mage, stealth character, etc.) and the race. That'll give you an idea of where to start, how many build points you have for the rest and which active skills to emphasize.
It also helps if you have at least a vague idea of your character's background to decide on how s/he learned the skills. This also helps for knowledge skills. For example, if I build a character who grew up with her parents, it makes sense she learned something about her parents' jobs so I typically give her at least a 2 in a couple knowledge areas that her parents worked in.
Taking flaws will give you extra build points, but be careful with them. Don't take something that you can't/won't roleplay just to get the extra points. It should be something that will cause problems for your character. And some flaws are finalized by the GM, so you might want to think twice about those if you don't want to give up that control.
Beyond that, Shadowrun is a very open system. There really isn't a right or wrong way to build a character and most skills end up useful at some point in the game. Even a knowledge like 20th century science fiction can come in handy. (I was in a game where we ran into Graboid-like creatures in the metaplanes.)