Did a quick search and the only difference I can found is the MKII has $125,000 insurance coverage and ~1800 joules protection.
The 2000 has $100,000 and ~1600 joule protection.
There might be more sutble differences, but that is what stuck out to me.
Each has 1 satellite and 2 coax pass-throughs & phone suppression.
Both will offer some protection from surges. Neither will protect from brown-out (low-voltage drops) or direct lightning hits to phone or satellite lead in.
Depending on your set-up, you may want to think about a power conditioner or battery backup with surge protection.
On the low end, you can get a couple of computer UPS units or go high end and look for a richard gray power conditioners. Some cost more than a whole home theater setup.