The reverse commute (peninsula to east bay in the morning, east bay to peninsula in the evening) is perfectly fine, as long as you don't have to take 880 anywhere. If you can avoid 880, that reverse commute can be serene and almost surreal (as you whiz past gridlock coming in the other direction every day).
There are a bunch of industrial parks right over the bridge in Newark that seem like great places for a new small company.