Unless you're building a very high horsepower motor I would go with the 2004R but it's totally up to you. Look here for all the details on a 2004R installation in a '69 Barracuda along with stock console shifter conversion. It worked out beautifully and I love it!!!
PS - I think the 700R4 is longer making it more difficult to get the trans mount to work. I have one of each (2004R and 700R4) in my garage and can check on the mount location. They are probably close since they are inter changable.
200R4 is shorter, so it may fit without floor mods. 700R4 (post-87 30 spline) is stronger. But the 700R4 has a freakishly low 1st gear so consider that if you are trying to get traction with street tires.
A 200R4 can take a LOT of hp when built right. You can install a 200R4 with no floor cutting but do have to make a small cut to get it to fit. Just look up the thread by Mopar To Ya. He installed on in his Dart Sport. Also with the 200R4 its all HYD which is big plus over the 700R4.
But remember...The 2004R weighs 9 lbs less and uses less horsepower to function. So you'll have less parasitic loss of power BUT the 2004R does have it's limits So if you're going to use it (2004R) behind a 500 HP (or less) motor you have the advantage of less weight and more power through put. So you'll get more power to your wheels. The 700R4 can probably handle more horsepower but it weighs more and sucks up more of your engines horsepower.
So it really depends on how much horsepower your engine has. My 200 is behind a mild 318 soon to be 390 stroker. The 390 will only have 375-425 HP so I'm not worried in the least.
In my case, I had a 2004R just sitting on my garage floor so my decision was easy.
Some of the disadvantages of the 700R4 are the width of the pan, the 2004R pan was barely able to get past my passenger side exhaust. The 700 is much wider in this area. The 200 body is also more narrow and requires much less cutting of your cross member. Also I would have never been able to run my factory shifter/console because the 700 body is too wide where the shifter linkage passes.
Treblig