oh hey you're from LA? Cool! I'm moving there in january. And since in LA you *need* to have a vehicle, I decided to get a bike.
As for the bikes, I would recommend you get the one *you* feel more comfortable with, since ultimately *you* will be riding it. You will also learn faster on a bike you're more comfortable with. If you ride the 250 for a few months and get bored of it, you should be able to resell it easily since the beginner bikes are in high demand (but that's just what I read, so take it with a grain of salt).
I was wondering myself about the highway use of 250. (just look at my previous posts on this forum) The impression I got is that 250 can theoretically do 75 mph and more, but it gets quite a workout from it. It cannot accelerate from 50 to 80 very well, so cars will start tailgating you and won't be able to do anything about it. The other problem is that ninja 250 is so light that you'll be affected by the crosswinds a lot. I can attest to that -- I rode ninja 250 at 50 mph and crosswinds made it rather scary. I actually moved to the center of the lane (which you are not supposed to do) because I was afraid of being pushed over. Of course ninja 500 is only about 80-90 lbs heavier so I'm not sure how that would help. Basically, as far as I can tell, you'd be a lot better off with a 500 on the highway. 250 can do it but not quite as well.
Anyway, clutch control is the hardest thing to learn on a bike (especially for me since I never drove a stick). What really helped me a lot is I rented a 250, took it to an empty parking lot and practiced starting and stopping. Did that for hours. Then practiced slow speed turns, for a few more hours. By the end of the day I was able to handle the clutch.
Another thing I would recommend is riding gear. I fell at my motorcycle course and scraped my knee pretty badly. And I'm glad I did! That made me realize the imprtance of proper riding gear, so I got full set of kevlar mesh (jacket and pants), as well as boots, gloves, and full-face hemet which I already had. Mesh is designed specifically for hot weather, so even in LA heat it should be rather comfortable. When riding the bike on the street, I felt a lot more confident knowing that if I fall it will hurt but I won't have to scrape my "O Ring" off the pavement. Or, as my instructor said "I will fall and hurt my "O Ring" but at least i'll still _have_ an "O Ring"!"

If I feel confident, I am, in fact, less likely to make a mistake and fall. It's a psychological thing.
Which brings me to my last point: you should take the motorcycle safety course if you haven't already. As someone else put it, you get a year's worth of experience in one weekend.
hope that helps. Good luck.
Eugene