You can get to Pisa in a bit over 2 hours from Civitavecchia without going through Rome, so that's not a bad day-trip. I believe I'm not alone, though, in commenting that Pisa is a quick sort of stop for most travelers. You'll be spending over 4 hours (that's just train time) to get there and maybe an hour or so to see the tower. Will it be worth it to you?
To get to Orvieto from Civitavecchia you must change trains in Rome. The trip will take about 2-1/2 hours, which is twice as long as it would take if you were starting out in Rome itself.
Hadrian's villa is east of Rome, not in the same direction as any of your other sights. I imagine it is doable from Civitavecchia but would surely be easier if you started from Rome, because the transportation for the villa (I'm guessing it's bus but I haven't checked) will surely originate in Rome.
Ostia Antica is located very near Fiumicino Airport, quite near Rome. I think you'd need to go into Rome to pick up the suburban train to Ostia Antica unless you found some sort of port-to-airport transportation and then got a taxi.
I think I'd rather base myself somewhere that has attractions of its own as well as day-trip possibilities. Orvieto would be one option.