If you do rent a car in San Diego to drive it to Ensenada, be aware that you need to find out a lot about the road situation and the traffic conditions at the international border coming back. if you aren't used to Tijuana, driving back across to the USA can be challenging. First, because the routes for how to get to the border crossings are not well marked and even occasionally completely misleading on the Mexican side. Second, because sometimes the wait times for cars crossing the border can be up to two hours. Third, because there are different kinds of lanes for the northbound vehicles (Sentri lane, Ready Lane, and "All Traffic") and it is not easy to tell which one you are going to end up in when you start into the border wait lines. You need to check the US immigration regulations to see which lane you have to come back in, but your passports might require you to be in the "all traffic" lanes instead of the "Ready lane".
The drive to Ensenada from Tijuana along the scenic toll road ("cuota") is really beautiful, and there are nice places to stop along the coast, but coming back north again, the border crossing in Tijuana (San Ysidro or Mesa de Otay) is never fun. If you have time and want more scenery, take the inland road from Ensenada and cross the border into the USA at Tecate - but do this driving all in the day time.