2 parts of your question
1. For CEC, FSW (Which I assume you are in?) and FST, No, you must go through Express entry. And EE is on top of FSW from before EE, so you must have 67 points in FSW system to qualify into the pool, and then high enough in EE-CRS points (varies) to be selected.
EE is not replacing anything, it's just one more hurdle in the way.
2. Depend on your province, PNP-EE streams might not be in place (I think as of now, only BC is giving nominations for EE)
Here if you choose to go thru PNP, You do have a choice, between EE and traditional paper application. The difference is time. I think BCPNP-EE stream is about 1-2 months from send in to nominate, then (As CIC promised) 6 months in CIC process. Old style PNP can take from 1.5 month to 9 month to get the nomination (depend on stream and province), then ~13-16 months in CIC's hand, depending on office. Huge timeframe difference.
IMO looking forward, the trend is most students will go thru PNP (EE or paper) as CEC-EE doesn't get a LMIA break, and that means your application is in the hands of others. (Remember EE is a competition system)