i ride Mission -> Niles -> Palomares regularly. The best time is mornings (no traffic) till around 2pm. After that it gets a little busy and there is one section that has no shoulder.
However, as folks have observed, it is watch a lot both in front for debris and back for cars (i rely a bit on Garmin Varia).
rarely i ride Mission -> Sunol.... mainly due to the two long curvy sections with no shoulders (the grove and around the bridges).
from Sunol -> Mission. This is my biggest concern. Speeds are high - for both cars and cyclist. and there is not enough reaction time (at least for me) to watch in front and then look back to react for debris!
The trail : BAH. they have promised this every stroll/walk/ride meeting. yeah sure.
Bike lane/Shoulder : i think they are sincere here. The engineer showed me the plans. There is shoulder widening..... HOWEVER, he did point out 2 concerns. (1) the ground is soft. the first time a truck rolls to the shoulder, he said there will be road damage that cyclists should watch out for. (2) debris - since its state highway, no particular city will clean/sweep it. He is concerned that tree debris, car garbage and glass/punk debris will be a big limitation.