One of the major drawbacks of the system is the amount of work the DM has to do when converting normal D20 monsters/NPC's to Ken's system. You have to do some homework.
If you keep the opponents to comparable NPC's and leave the huge monsters few and far between, the players are actually at an advantage under the system, I think. In the 3 levels we used it for, only one PC was lost. Good, for my campaigns.
Someone mentioned about armour penetration. You may want to expand on Ken's list. I want to say that something obvious was left off, perhaps a crossbow bolt. It's easy to assign penetration values for things like that, though. Just work off of what is already there. Be prepared for your players to use a heavy pick (bec de corbin) as their weapon of choice, too (high armour penetration value)
Overall I liked the system alot, but it was some work - especially if you have a combat intensive campaign. And by the way, yes, the two can coexist. As long as the PC's are moderately prepared and use sound strategy, they can engage in several battles against equals and come out okay. It's when you throw in a huge troll or something like that at your PC's that they will be put to the test.
One other tip. Use the "odds are one" system for magic. This way you don't have to change the spells as listed, but their damage is brought down to the system numbers (while still retaining their lethality). Use the same "odds are one" system for thieves and their sneak attacks, too. I think it's superior to the mechanic Ken put in. I think I even e-mailed him with the suggestion, and he thought it was a great alternate to the sneak attack system included in the rules.
Hope that helps. It's a great alternate to the combat system in the players handbook. I'm glad we tried it, too. Thing is, you can easily "switch back" to the other system. Just have your players roll their normal (3e) hit points etc. and keep them off to the side, so to speak. That way if it doesn't work out, you can just pick things up under the regular system.