My computer wasn't letting me quote anything last night. Really strange!
If I could only have 1 Daytona, I'd have one with the El Primero based movement, and I'll explain why later. I think you have to ask whether you are buying something to wear but also as a collectible, or whether you are going to use it as a daily wearer and you want the newest maybe most rugged version on the market. The current Daytona has a much longer power reserve 72hrs vs roughly 42 (those are without the chronograph function activated). The newer one also has larger easier to see luminous markers, but they are a bit clumsy looking compared to the old one. The new movement has fewer parts so servicing is supposed to be easier/less complicated (although unless you are servicing it yourself, who cares?). In addition, the newest Daytonas have a bracelet with all solid links (although I owned Rolex watches on hollow Oyster bracelets for years and they held up very well). Although no one knows the production numbers for particular models of Rolex per year, most people believe that once Rolex was making Daytonas with in house movements, the production numbers increased drastically as they were no longer dependent on what others could supply them.
Both are nice solid watches, I've used each in the past as daily wearers. My prefernce is for the El Primero based watches largely due to its design and appearance ( and knock on wood I've never had a problem with them). Although they use the Zenith El Primero as a base movement, they are vastly different. The number of beats per hour was changed, and supposedly there are approximately 200 modifications made to the movement before it became Rolex Cal 4030. The first in house Daytona I had, after sitting for about 4-6 months when I activated the chronograph, the minute subdial went crazy and would jump in intervals of 3 minutes, 5 minutes etc even though the large chrongraph sweep hand had only made 1 revolution. It was fixed under warranty, so not a big deal, but it was the only time I've had an issue with a new Rolex...but don't let that make or break your decision. My current inhouse Daytona purchased new in 2005 is fine.
Overall, I perfer the appearance of the Zenith El Primero watch. Its just a more classic look when you put them side by side. The thin hour/minute hands and luminous markers around the dial are smaller and more elegant making the watch a bit more versatile (I think it looks better with a suit than the current model). I also prefer the centered look of the subdials on the Zenith version. The inhouse model, Rolex shifted the Subdials upward by a few degree in an effort people say to make it tougher to make copies. I also think the white/cream subdial trim rings on the black dial and the black subdial trim rings of the white dial look more elegant and are easier to read than the silver subdial trim rings of the current version. I also prefer the continuous seconds at 9 than at 6...I think it makes it a bit more interesting (tons of watches have it at 6). Then you can get into the various years if you want somewhat rare one, where the word Cosmograph is separated from the other text on the dial, or different fonts, or the different bezel only to 200 units on the early models (rather than 400).
Either should provide you with a great watch that you will enjoy for many years. If you choose to go for an inhouse movement opt for one made around 2005 or later with the fat hands. The early ones made from 2000-about 2004, just looked mismatched using larger luminous markers around the dial with the original thin style hands from the prior Zenith based model. Either get a Zenith based model all of which had thin hands & thin markers, or get the later inhouse version with fat hands and fat markers.
I hope that helps. If you have a more specific question that I didn't answer just let me know and I'll try to address it.
Dino, would you mind taking a pic of your El Primero and in-house movement'ed Daytonas side-by-side, please?