I was researching the same thing a few months back and I found one fact that was staggering between the two. The downside is, I don't remember it!
I don't think the 4M series can be had with the 3PT down-force kit that gives you hydraulic down pressure on implements. Also, the loader joystick on the 4M is positioned in a weird spot up on the right hand side of a steel plate. On the 4R series, it is in a much better location for the operator, coming out of the floor by the right side fender. There are other differences, but most of them minor. Each person will feel differently about this, but for myself, if I was going to spend $30,000 on a 4M, and a 4R was only $4,000 more, I would spend $34,000. An extra 10% or so isn't that bad.
You can get a 4052M for the same price as a 3046R. I would take the 4M over the 3R when money is equal. You get a much larger machine with way more capacity, and substantially more engine. One major downside to the new 3R and 4R machines is the pricing. John Deere really upped their cost on these because of the new emissions equipment needed to get the diesels to meet Tier4 standards. Naturally, John Deere passes this onto the consumer, even though they could have EASILY absorbed that cost, and still made boat loads of cash.
I honestly believe that on a $40,000 tractor, there is probably $15,000 - $20,000 total profit in there. I have been involved in business in the last two years and the standard amongst companies seems to be around 50% return in profit, as far as retail type stuff goes. IMO, that should not be allowed. That is down right stealing from us hard working average guys!