Im a two stroke guy, so I vote for the 2stroke! But people either love them or hate them. I have rode both the 400 scrambler and 500 scrambler, BUT were you are going to ride will be most important. So lets talk...
First, you need to find out if the areas you plan to ride will allow 2-strokes. Sad as it is, many areas are starting to outlaw 2-stroke anythings because of the smoke and noise they make. If this is going to be a problem, go 4-stroke, if not, then its of no concern.
400 Scrambler-
Im not sure how familiar you are with any of this, so I will start from the basics. 2-strokes are generally lighter (engine wise) then 4strokes. Maintenance tends to easier and cheaper on a 2-stroke, but needed more often. You will need to rebuild the top end of a 2stroke a lot more then a 4stroke. (Most of the time). But, there are no valves to adjust, there is no oil changes (gearcase and diffs, yes, but engine case, no). 2strokes are simply, and easy to work on. You will have to front the cost of 2stroke oil which can be expensive to buy, but, a big jug (like 1 gallon) will last you a very long time. It is going to smoke, it is going to be noisy, but thats a typical 2stroke. Acceleration on a 2stroke is awesome! I would be comfortable to say the 400 scrambler will out accelerate the 500 scrambler. Top speed will be close to a draw on stock machines. Two strokes tend to not have any bottom end power, they do not liked to be lugged. The joke is, they are either no throttle or wide open throttle, thats the only two things they know. It is a half truth though. They get up and go well. If you are going to be riding in open areas, sand dunes, flats, deserts, or open trails, a 2stroke is a good machine. Tight, technical riding, you might be better off on the 4stoke, it will be more forgiving and easier to handle (this is where the 4strokes ability to have more useable bottom end power comes in). Not to say you cant ride technical on a 2stroke, you certainly can! It just takes much more patience and skill.
Reliablilty-Good if you do proper maintenance. It will need more engine work then a 4stroke in its lifetime, but its easier and cheaper to do then any 4stroke. That that kinda washes each other out in my book.
Power- Great, in my book, plenty
Acceleration- Again, great, probably will accelerate to top speed a little faster then the 500 scrambler
Speed- Stock for stock, going to be about a wash. Plenty of top speed for most types of trail riding. Aftermarket parts can bump this up.
500 Scrambler-
Now you are looking at things like valve adjustments and oil changes, neither are a huge deal though. Acceleration is still good, it will be much quietier and wont(read: shouldn't) smoke out the exhaust. Aftermarket parts are probably easier to come by for the 500 since there are much more 500 scramblers then their 400 sized brother. The big advantage is much more useable low end power. Tight technical terrain will be a favorite of the 500 scrambler.
Reliablilty- Again, good, if proper maintenance is done
Power- Good, will probably want more after you ride it (who doesnt want more?) And this is a machine with aftermarket parts to follow
Performance- Good, just like its 400 sized brother, it is a straight rear axle, so the suspension will not be a smooth as and IRS machine.
Speed-Good, probably a hair slower and acceleration compared to the 400.
The Scrambler is a good machine that hasnt changed in quite a while. It is easy to work on. I would take either one. They are pretty close. Most people perfer 4strokes, so the 400 kind of faded out of style to make room for the 500. I still enjoy a 2stroke quad. They are simple, with brutal power. Just fun! The 500 scrambler is more gentle, but still can be a monster. Both are a step below a predator or outlaw as far as a true sport quad goes, but thats not the design intention.
As you noted, its 4x4. Its a little more heavy, not quite the suspension travel numbers, not quite as brutal acceleration as the sport qauds, (because of the CVT tranny). But it is a very nice blend between utility quad and sportquad. I know it sounds cliche, but its something a newbie can enjoy all the way up to a seasoned rider. Its a good machine all around. Either of them.
I hope I gave you enough info to make the choice yourself.