The Motorrad alternator is basically the same type of alternator as the stock system you have in your bike now but a lot beefier so has more output. The advantage of doing this upgrade is that it's a drop in replacement but has the disadvantages of that system, wearing brushes, heat generation in the stator/rotor. One other trap in this type of system is that if the generator lamp in the dash fails the system won't charge. Motorrad supplies a bypass for this reason but they recommend a voltmeter on the bike.
The Endurolast alternator is a brushless alternator system with a permanent magnet. Installation is slightly different as the rectifier and regulator is one unit so it needs to be mounted in a different place on the bike. Having no brushes to wear out is a good thing.
They both put out around the same output at high RPM but I don't know which type of alternator has the better current output at lower RPM's and this could be part of your problem if you are riding in city stop/start traffic a lot.
As mentioned earlier the stock system should be adequate providing it's working correctly and you have no additional equipment you are trying to power (extra lights, heated vests, etc) but as I found out the official output may not match reality.
We use heated vests in winter on our bike and I did have charging problems with the stock system so about 4 years ago I fitted a Motorrad alternator and found it to be very good. I also fitted a voltmeter as well. I would recommend putting a voltmeter on your bike before spending the money on a new alternator as it will show up any existing problems you might have. It took me about 8 hours to fit the new alternator and you need a fairly hefty soldering iron. The instructions were quite good and if I did it again it wouldn't take nearly as long.
There are some stock faults on the original charging system including cracked earth leads, faulty board mounts, loose connections and dead rectifiers that could be the cause of your problem.
One problem with both systems is that they make the bike non standard so if it dies while you're in the middle of nowhere you have the problem of parts etc.
Finally, have a look at this link (and other from Bob's site) about problem solving the charging system
BMW Airhead Motorcycle Alternator Repair
And this one for some comparisons between the charging systems
Enduralast or Omega Charging upgrade revisted - ADVrider
Hope this helps