Well, from one "ace" to another, the AVL does have several improvements to the engine, compared to the iron-barrel models.
The AVL has an alloy barrel which definitely helps cooling.
Better oil pumps.
Steel con rod with roller big end.
The 5 speed gearbox is better, but they are also on the later iron barrel models.
Electronic ignition reduces maintenance.
However, there are also some limitations included.
One of them seems to be that the crank-mounted electronic ignition has no ability for re-timing. It isn't a problem if you keep everything stock. If you play with compression increases, you might run into a spot where you can't retard the ignition correctly for the compression increase. I find this to be a serious drawback from my point of view as a modifier.
The con-rod is steel, and has a roller big-end bearing, which is something that we iron-barrel guys like to do to our bikes. That's a good thing.
But, they unfortunately made the roller bearings run directly in the rod, instead of making a pressed-in bearing race, and thus the roller bearing has failure problems. This is curable, but it requires an engine tear-down.
There used to be issues with getting bottom end replacement parts for the AVL, but apparently that has been overcome, because I see people doing things now with the AVL bottom ends.
The gear-type oil pumps are a great improvement for oil delivery in the engine.
But they aren't a positive displacement type pump, so oil drainback can and does cause some wet-sumping issues when the bike is parked for a length of time. Not a big deal, but it can smoke out the exhaust for a minute or two after starting up from a long rest.
The sprags are the same with the iron barrel and the AVL. Very common problem for both types of engines, and not alot can be done about it.
So,there's some good things and some not so good things that came along with the changes to the AVL.
For the iron-barrel, it has been around for ages, so everything that needs improving has aftermarket parts available readily to improve it. It's a more antique design, but it has been raced alot over the years, and it can be perked-up in power very well.
The 5-speed gearbox is better than the 4-speed box, but the 4-speed isn't too bad, and a right-shift kit and sealed bearings for oil in it can make it nicer. A close ratio gear set is available to improve the ratio gap between 3rd and 4th.
However, if there's a choice, the 5-speed is a better gearbox. The iron-barrel later models have the 5-speed gearbox.
A 2003 iron-barrel model is a very good year, which has the better breather.
I have to admit that I favor the iron-barrel model. I have one and I like it, and it is easy for me to modify and get desired results.
I personally feel that the AVL didn't achieve all the improvements that they could/should have achieved with the re-design, and it fell short.
Its still a good engine, with improvements over the iron-barrel, but the little issues that they "added" along with the improvements were irritating, and didn't have to be there. They could have solved these issues pretty easily, but didn't.
Overall, with a stock bike of either type, it's a good ride, and the AVL has a slightly higher safe cruising speed by a couple of mph.
For me personally, I'd pick the 2003 iron barrel model without hesitation. That's a good year for the iron-barrel models.