I'll jump in here with my experiences on progressive presses. I started shooting IPSC in 1988, and shortly after, I purchased a Lee Pro 1000. I retired that press about 3 years ago when I upgraded to a Dillon 650 . Personally, I like auto indexing, I feel that it is an added safety measure. To me, manual indexing is always the place that a double charge can happen. All it takes is one minor brain fart to double charge a case. Now on to my experiences with the 2 presses.
The Lee loaded many 10's of thousands of rounds of 38, 9, 40 and 45 ammo. The press did good, but there were a few quirks that I never got worked completely out. First, it seems that out of every 100 rounds, I always had 2 or 3 that the primers went in either upside down or sideways. The little plastic primer feed chute really never fed the primers real smoothly, either. I was always tapping on either the feed chute or the primer holder to keep them feeding. I had the case feeder tubes and they did good for the most part. All in all, it was a good press for the ~$100 or so that I paid for it, but that is what I had, a hundred dollar machine. What few times I had a problem, a part wore out, or I broke something, I always had to pay for it. No freebies. Seems like I did good to load 200 or so rounds per hour. Another thing that hindered me on the Lee machine was that I liked to use the Lee Factory Crimp die after I loaded, just to make sure the round was as close to in spec as I could get it. Since the Pro 1000 only had 3 places for dies, I had to do this as a seperate step. Now, the Pro 1000 does have 4 hole turrets, I think.
About 3 or 4 years ago, I decided to upgrade to the Dillon 650. That was my choice since I wanted auto indexing. I went whole hog with the case feeder, powder check and all. I have it set up to load 9mm, 40, 45, 223 and 308. Any other calibers I shoot, I load on a Lee Turret Press. I don't shoot enough of them to justify progressive loading, as they are mostly hunting loads. I can change calibers on the 650 in about 15 minutes, I really haven't timed myself, but it doesn't take long. Caliber conversions are a little pricey, but it is good quality. If you really get into it, there are several parts that can be moved between calibers to help save a little money. Since I was already loading these calibers on the Pro 1000, I still use my Lee Dies with the Dillon press. As for loading rates, a few weeks ago, I loaded 1100 rounds of 40S&W in 90 minutes, including about a 10 minute break at about half way to reload primer tubes and get a drink. This past weekend, I loaded 1800 rounds of 9mm in less than 3 hours, including breaks and primer tube relaoding. 223 and 308 I can load at ~400 to 500 per hour. This was just working at a steady pace, not trying to set any records. I inspect every round after I finish, and so far, in the last 3 years, I haven't found one upside down primer. Now this isn't to say that there isn't a kink every once in a while, there is. The Dillon isn't foolproof, it is just light years ahead of the Lee 1000. I have broke 2 parts, it was 100% my fault both times, but they were insulted that I offered to pay.
All in all, the Lee is a good machine, it will get your ammo loaded, but won't be fast. I can't bi*ch too much about it, becaues I used it for about 13 or 14 years and loaded literally truck loads of ammo on it. You might have some quirks you have to work around. If you can afford the more expensive Dillon, by all means go for it. If you get the 650, you will need the case feeder. If you don't get the case feeder, go with the 550. Another Dillon to look at if the 550 and 650 is a little out of your range, but you still want a Dillon, is the Square Deal B. It uses Dillons own proprietary dies, and loads handgun ammo only, but is still a progressive with auto index. I haven't used one personally, but several of the shooters in my club do use them and really like them.
Good luck on your choice and safe reloading.