I agree with most that you'll probably really like the new sled - but, a good running, stock 2000-2003 XCR 800 will definitely beat a stock Apex ER.
If having the fastest sled is your #1 requirement, and there are others that ran close to your XCR 800, you might be a little disappointed on the lake. Of course if speed is the goal, if you add a turbo or supercharger to an Apex no one can touch you at all.
On the other hand, the Apex' motor is incredibly smooth and has very good throttle response (similar to the XCR) and these motor always run great. While the XCR has a great motor also, on a warm day they were noticably down on power compared to cold, while the Apex runs great always.
Several of my buddies sold their XCR 800's for their current Apex ERs and I sold (actually I'm still trying to sell) my well tuned/built '97 Storm 800 (it ran side by side with the well tuned XCR 800's) for Yamaha 4-strokes.
All of us notice the decrease in top speed (for us we found a fairly big drop), but none of us want to go back. Acceleration wise they are very close with studs.
The biggest improvement we found was the fuel economy. The Apex, while still not great on gas, gets almost twice the fuel mileage of the XCR 800. The next biggest improvement is comfort and ergonomics. On the Apex you can ride far longer and far more hours before you tire.
Basically the number of hours of fun you can have on an Apex is far greater than the number of hours of fun you can have on an XCR 800.
If you're an aggressive rider, one thing you probably will not be happy with is the rear suspension is too soft. At first you'll be blown away at the smooth ride, but once the trails get mature you'll find it way to easy to bottom out until you install a heavier rear spring. A couple of things to watch out for, especially if you like to run long lakes wide open, is idler wheels delaminating and chaincase oil leaks. Yamaha has an updated wheels and a new chaincase cover that fix these weak areas.