I've had two train experiences (with bikes), one good and one not-so-good. The bad one was this summer, coming back from Solana Beach. There were mechanical problems, so they were one train behind. We waited about 1.5 hours for a train. Also complicating things was the Del Mar Fair and horseraces right during that time, so the trains were unusually crowded.
The good experience was during last month's Burrito Century. We rolled into San Diego 20 minutes before the next train left. We were ticketed and wisked on the train almost immediately. We even were offered a group rate since we had more than 10 riders. Luckily the downtown SD station is one stop past the Old Town station, so the drunk football goons (there was a Chargers game that day) got on after us. So we had plenty of seats.
Overall, I think Amtrak is great for local travel. Of course, by virtue of it being mass transit, it's not perfect. If I had surgery, or some other important event planned for later the same day, I wouldn't bank on the train being on time. That said, I find it a cheap and fun way to go! But if you have time constraints, be cautious, and leave plenty of time.
There are issues sometimes with bikes -- they claim a pretty low number as the maximum allowed on each car, but they have always been accomodating, and we've put more bikes on a car than the stated "maximum."
You can take bikes on and off at any stop, far as I know.
If you have other questions, feel free to PM me. I can go on and on....
<< no sig at this time >>