Thinking of getting a Yaris in the not-too-distant future

[jingles]

With one more year of college left, I don't have the cash to replace my hand-me-down, gas-guzzling Buick just yet, but I'm already getting eager to do so and looking at what my options will be in about a year. As my main concerns are reliability, economy, and total cost of ownership, I'm looking at the Yaris, Fit, Civic, and Corolla, with a bit of a bias toward the Toyotas since my dad's 2008 Highlander is chugging along just fine at ~220k miles with only one trip to the dealership for anything besides scheduled maintenance. So, since it looks like the US Yaris for the next model year is remaining unchanged except for the addition of daytime running lights, I figured I'd fire away:

• Do most people find the LE a worthwhile upgrade over the L? I can see things like the split-folding rear seat and steering while audio controls being handy, but it looks like cruise control is fairly easy and cheap to add on my own, and I'd almost prefer to have crank windows--a power window issue was the reason why my dad's Highlander had to be taken in.
• As someone who's only driven an automatic before, is there any reason I should go for or avoid the manual transmission if I decide on the L? I'd certainly like to learn how to drive with three pedals, but I don't know yet if I'd want to use one regularly (or learn on the Yaris's) and the auto gets pretty good mileage anyway. It's cheaper to replace a clutch than an auto, of course, but Toyota transmissions do seem to last ages.
• In your opinion, are there any real reasons to go with a Corolla over the Yaris, or look at the Hondas instead?