Here is a basic break down from an airsoft perspective that you are looking for. Some of it has already been said but I thought I would condense it all into one place.
Barrel LengthIn general, a longer barrel provides better range and accuracy than a shorter barrel. Of course there are exceptions to the rule. It all depends on how your gun is modified.
Gun LengthShorter guns are easier to maneuver with (Especially when exiting from inside a vehicle). Some versions like the Para can actually be heavier though. Full length guns tend to be visually more intimidating.
StocksA full length stock allows you to carry a large battery. This can be very important for a SAW gunner, especially in a large game. Para style SAWs are forced to use smaller batteries in the front grip which generally have half the capacity of a battery that can be used in a full stock. Also, by having the battery in the stock gives you better gun balance. The Mk-II stock is also more comfortable when shouldering (Unless you have short arms) or in the prone position. Short stocks tend to be an advantage in thick bush, buildings and exiting vehicles. Also, you can usually shoulder a SAW for a bit longer since you can pull in it to your shoulder and support it better. This may very depending on how long the users arms are.
BatteryOne exception to the battery is that in most M249s, you have the option of placing the battery in your ammo box. In most versions such as the Echo-1, A&K and Classic Army, it requires you to run wires from your ammo box to your gun. The Pro on this is it allows you to carry a very large battery like the Mk-II but still have a compact gun. Also by having the battery in the ammo box it provides better weight distribution. The Con for this type of set up is if you only have one of these ammo box and it goes down, your done for the day unless you want to hump another big box mag as a back-up. By having your battery in the stock or front grips, you can uses M-4 Hi-Caps as back up or you can use a nut sack.
Ammo BoxMost LMGs/SAWs, you only have one choice in ammo boxes. The M249 and a few other you have several choices. In the case of the M249, you have the large ammo box (2,500~4,000 rnds) and the (medium) nut sack (1,500~2,500 rnds). The differences are obvious. The large ammo boxes allows you to carry more firepower but is bulky and heavier (due to the weight of the BBs). The nut sack smaller size allows you to move lighter with more maneuverability but at reduced ammo capacity. As you already know you can use the M-4 Hi-Cap as well. I usually carry a few as an emergency back-up should my box mags go down.
Below are pictures of several variation to make it easier to compare. The bottom 3 pics are my gun. The bottom pic is my current version. I call it a Mk-II Mod-2. I went with this version because I wanted a long barrel for better range and accuracy but still wanted an adjustable stock. My arms are a tad on the short side and the full stock made it difficult to shoulder for a long period of time. The G&P Improved Collapsible Butt Stock allows me to shorten it when shouldering but extend it when in the prone. This forced me to move the battery in the front underneath the barrel. I was able to combine two 7.4 1,400 mAh LiPo batteries to give me a total of 2,800 mAh which is usually more than enough for one day, unless you're playing in a large game. The only disadvantage is with the RIS there is no quick battery change and I have to carry an Allen wrench with me to be able to access the battery.
Ultimately, it all depends on what you like.
Two thing I do strongly recommend. One, invest in a good padded SAW sling. It will greatly reduce the fatigue of carrying one around for any long period of time. Two, if you're going to get an M249, get a Classic Army. Brand wise they make the best ones.
Para Version
Mk-46 MOD-0
First Upgrade
M249 Mk-II MOD-1
Current Configuration
M249 Mk-II MOD-2
