Hmm...I think to get to the same equipment level in the Prius (inclusion of Navi, since the OP asked about it), you're looking at package #7, along with the optional floor mats, bringing you to 26,700 or so. Package 8 adds in leather seats for an additional $1400 or so - if you added that in for a 'fully loaded' car, you'd be at
just over $28,000. But since (factory) leather isn't available in the Civic, I'll leave that off for now.
Now, to address the original poster's questions:
1. I believe the Prius is estimated to be eligible for a $3400 tax credit, while the Civic Hybrid's credit is estimated at $2300. So... post-credit, you'd be looking at approx $23,300 for a Prius w/ Package #7, vs $21,600 for the Civic. This includes destination charges, but not TTL, of course - that varies by locality. Don't assume that you'll get the full credit by end of summer for the Prius - Toyota has already warned that they may sell > 50,000 hybrids across their product line by then (I'd agree) - when that happens, your $3400 will be (at least) halved to $1700.
2. "cost, style, latest reviews, differences in reliability, personal biases, etc. etc.). If you had to make a choice, which would it be?"
Well, cost is above. Style is subjective - basically, if you want the car to be 'noticed', the Prius is better at that. It is a hatchback, so you have the increased cargo capability and folding rear seats. Rear-seat headroom can be a factor with some people.
Latest reviews are all very favorable for the Civic Hybrid (& all trim levels), since it's been redesigned. If you want to drive 'the latest sheetmetal', then Civic scores here, as the current Prius dates to 2004 or so.
Differences in reliability - About equal. I'll trade you a Civic battery replacement for a stalling Prius.
What I'm saying is that there will always be a small number of cars with problems. But both 'Yota and Honda score very well on the JD Powers reliability index, relative to their competitors.
Personal biases - you've read through a few of them here. For me, the biggest factors between the two would be interior room & ergonomics (you spend your time *inside* the car, after all), safety, handling / ride, and then best fuel economy, if within 10% (since we're buying these cars with that being at least half the reason for purchasing one), followed up by 'less polluting'. So for me, the Honda won out - but I will admit, I've been buying Hondas for a long time now, and I do have a bias toward them.
3. I can't answer this as well as some of the Prius owners, but I would think a six-month wait for exactly the color / equipment you wanted would not be out of the question (six-month waits used to be very common for the car). If you're willing to compromise on color and / or features, you'll get the car quicker.